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\u90a3\u4e48\uff0c\u4e3a\u4e86\u4ece\u7edf\u8ba1\u5206\u6790\u4e2d\u83b7\u5f97\u6709\u610f\u4e49\u7684\u7ed3\u679c\uff0c\u6d88\u9664\u6279\u6b21\u6548\u5e94\u5c31\u662f\u5fc5\u8981\u7684\u3002\u5982\u679c\u7ec4\u5b66\u5b9e\u9a8c\u8bbe\u8ba1\u5f97\u5f53\uff0c\u6279\u6b21\u6548\u5e94\u4e0e\u611f\u5174\u8da3\u7684\u6548\u5e94\uff08\u5904\u7406\u3001\u75be\u75c5\u3001\u7ec6\u80de\u7c7b\u578b\u7b49\uff09\u4e0d\u76f8\u6df7\u6dc6\uff0c\u6240\u8c13\u7684\u6279\u6b21\u6548\u5e94\u4fee\u6b63\u7b97\u6cd5\uff08BECAs\uff09\u53ef\u4ee5\u7528\u6765\u6d88\u9664\u6216\u81f3\u5c11\u51cf\u8f7b\u7cfb\u7edf\u504f\u5dee\u3002\u56e0\u6b64\uff0c\u8fd9\u4e9b\u65b9\u6cd5\u5bf9\u4e8e\u6574\u5408\u6765\u81ea\u4e0d\u540c\u5b9e\u9a8c\u5ba4\u7684\u6570\u636e\u6216\u5728\u4e0d\u540c\u65f6\u95f4\u6d4b\u91cf\u7684\u6570\u636e\u975e\u5e38\u6709\u7528\u3002\u8fd9\u4e9bBECAs\u4e4b\u4e00\u662fARSyN\u65b9\u6cd5 [<\/span>1<\/span>]\uff0c\u5b83\u4f9d\u8d56\u4e8eANOVA-Simultaneous Components Analysis (ASCA)\u6846\u67b6\u5c06\u7ec4\u5b66\u4fe1\u53f7\u5206\u89e3\u4e3a\u5b9e\u9a8c\u6548\u5e94\u548c\u5176\u4ed6\u4e0d\u9700\u8981\u7684\u6548\u5e94\u3002ARSyN\u5e94\u7528\u4e3b\u6210\u5206\u5206\u6790\uff08PCA\uff09\u6765\u4f30\u8ba1\u7531\u6279\u6b21\u6548\u5e94\u5f15\u8d77\u7684\u7cfb\u7edf\u53d8\u5316\uff0c\u7136\u540e\u4ece\u539f\u59cb\u6570\u636e\u4e2d\u5c06\u5176\u53bb\u9664\u3002 BECAs\u4f20\u7edf\u4e0a\u5e94\u7528\u4e8e\u6d88\u9664\u76f8\u540c\u7c7b\u578b\u7ec4\u5b66\u6570\u636e\u4e2d\u7684\u6279\u6b21\u6548\u5e94\uff0c\u4f8b\u5982\u57fa\u56e0\u8868\u8fbe\u3002\u7136\u800c\uff0c\u7528\u9002\u5f53\u7684\u5b9e\u9a8c\u8bbe\u8ba1\u4ece\u5355\u4e00\u7c7b\u578b\u7684\u7ec4\u5b66\u6570\u636e\u4e2d\u6d88\u9664\u6279\u6b21\u6548\u5e94\u76f8\u5bf9\u7b80\u5355\uff0c\u4f46\u5728\u5904\u7406\u591a\u7ec4\u5b66\u6570\u636e\u96c6\u65f6\u53ef\u80fd\u53d8\u5f97\u4e0d\u53ef\u884c\u3002\u5728\u591a\u7ec4\u5b66\u60c5\u51b5\u4e0b\uff0c\u6bcf\u4e2a\u7ec4\u5b66\u6a21\u6001\u53ef\u80fd\u7531\u4e0d\u540c\u7684\u5b9e\u9a8c\u5ba4\u6216\u5728\u4e0d\u540c\u7684\u65f6\u95f4\u70b9\u6d4b\u91cf\uff0c\u56e0\u6b64\u662f\u5728\u4e0d\u540c\u7684\u6279\u6b21\u4e2d\u83b7\u5f97\u7684\u3002\u5728\u8fd9\u79cd\u60c5\u51b5\u4e0b\uff0c\u6279\u6b21\u6548\u5e94\u4f1a\u4e0e\u201c\u7ec4\u5b66\u7c7b\u578b\u6548\u5e94\u201d\u6df7\u6dc6\uff0c\u65e0\u6cd5\u4ece\u6570\u636e\u4e2d\u79fb\u9664\u3002\u7136\u800c\uff0c\u5728\u67d0\u4e9b\u60c5\u51b5\u4e0b\uff0c\u591a\u7ec4\u5b66\u6279\u6b21\u6548\u5e94\u53ef\u4ee5\u5f97\u5230\u7ea0\u6b63\u3002MultiBaC\u662f\u7b2c\u4e00\u4e2a\u5904\u7406\u591a\u7ec4\u5b66\u6570\u636e\u96c6\u4e2d\u6279\u6b21\u6548\u5e94\u7ea0\u6b63\u7684BECA\u3002MultiBaC\u53ef\u4ee5\u6d88\u9664\u4e0d\u540c\u7ec4\u5b66s\u7684\u6279\u6b21\u6548\u5e94\uff0c\u524d\u63d0\u662f\u81f3\u5c11\u6709\u4e00\u79cd\u5e38\u89c1\u7684\u7ec4\u5b66\u6570\u636e\u7c7b\u578b\u5305\u542b\u5728\u6240\u6709\u6279\u6b21\u4e2d\u3002 <\/span>MultiBaC<\/span>\u5305\u5305\u542b\u4e24\u4e2aBECAs\uff1a\u7528\u4e8e\u4ece\u5355\u4e2a\u7ec4\u5b66\u6570\u636e\u7c7b\u578b\u4e2d\u6821\u6b63\u6279\u6b21\u6548\u5e94\u7684ARSyN\u65b9\u6cd5\u548c\u5904\u7406\u591a\u7ec4\u5b66\u6d4b\u5b9a\u6279\u6b21\u6548\u5e94\u95ee\u9898\u7684MultiBac\u65b9\u6cd5\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n\u5355\u4e2a\u7ec4\u5b66\u6570\u636e\u6279\u6b21\u6548\u5e94\u7684\u4fee\u6b63<\/strong><\/span><\/p>\n\u5173\u4e8eARSyN<\/strong><\/span><\/p>\nARSyN\u65b9\u6cd5\u6982\u8ff0<\/span><\/p>\nARSyN\uff08ASCA\u7cfb\u7edf\u6027\u566a\u58f0\u53bb\u9664\uff09\u662f\u4e00\u79cd\u7ed3\u5408\u4e86\u65b9\u5dee\u5206\u6790\uff08ANOVA\uff09\u548c\u4e3b\u6210\u5206\u5206\u6790\uff08PCA\uff09\u7684\u65b9\u6cd5\uff0c\u7528\u4e8e\u4ece\u4f30\u8ba1\u7684ANOVA\u6a21\u578b\u4e2d\u9274\u5b9a\u51fa\u7ed3\u6784\u53d8\u5f02\uff0c\u8fd9\u4e9b\u6a21\u578b\u9488\u5bf9\u7684\u662f\u5b9e\u9a8c\u548c\u4e0d\u9700\u8981\u7684\u6548\u679c\u5bf9 \u7ec4\u5b66\u6570\u636e\u77e9\u9635\u7684\u5f71\u54cd\u3002ARSyN\u53ef\u4ee5\u53bb\u9664\u4e0d\u9700\u8981\u7684\u4fe1\u53f7\uff0c\u4ece\u800c\u83b7\u5f97\u7ecf\u8fc7\u566a\u58f0\u8fc7\u6ee4\u7684\u6570\u636e\uff0c\u4ee5\u4fbf\u8fdb\u884c\u8fdb\u4e00\u6b65\u7684\u5206\u6790\uff08<\/span>1<\/span>\uff09\u3002\u5728<\/span>MultiBaC<\/span>\u5305\u4e2d\uff0cARSyN\u88ab\u7528\u4e8e\u8fc7\u6ee4\u4e0e\u5df2\u8bc6\u522b\u6216\u672a\u8bc6\u522b\u7684\u6279\u6b21\u6548\u5e94\u76f8\u5173\u7684\u566a\u58f0\u3002\u8fd9\u79cd\u9002\u5e94\u6027\u88ab\u79f0\u4e3aARSyNbac\u3002 \u5728ARSyN\u65b9\u6cd5\u4e2d\uff0cANOVA\u6a21\u578b\u5c06\u6bcf\u4e2a\u56e0\u7d20\u5728\u5b9e\u9a8c\u8bbe\u8ba1\u4e2d\u8bc6\u522b\u7684\u4fe1\u53f7\u4e0e\u6b8b\u5dee\u5206\u5f00\u3002\u8be5\u7b97\u6cd5\u53ef\u5e94\u7528\u4e8e\u591a\u56e0\u7d20\u5b9e\u9a8c\u8bbe\u8ba1\u3002\u5982\u679c\u5df2\u77e5\u6bcf\u4e2a\u6837\u672c\u6240\u5c5e\u7684\u6279\u6b21\u4fe1\u606f\uff0c\u5219\u6a21\u578b\u4e2d\u7684\u4e00\u4e2a\u56e0\u7d20\u53ef\u4ee5\u662f\u6279\u6b21\u3002\u5728\u8fd9\u79cd\u60c5\u51b5\u4e0b\uff0cANOVA\u6a21\u578b\u5c06\u7528\u4e8e\u5c06\u6279\u6b21\u6548\u5e94\u4e0e\u5176\u4ed6\u6548\u5e94\u548c\u6b8b\u5dee\u5206\u5f00\u3002\u56e0\u6b64\uff0cPCA\u5206\u6790\u5c06\u68c0\u6d4b\u5230\u7531\u4e8e\u6279\u6b21\u6548\u5e94\u800c\u53ef\u80fd\u5b58\u5728\u7684\u7ed3\u6784\u5316\u53d8\u5f02\uff0c\u5373\u7531\u89e3\u91ca\u6570\u636e\u603b\u53d8\u5f02\u4e2d\u7ed9\u5b9a\u6bd4\u4f8b\u7684\u4e3b\u6210\u5206\u8bc6\u522b\u7684\u53d8\u5f02\uff0c\u7528\u6237\u53ef\u4ee5\u8bbe\u7f6e\u8be5\u6bd4\u4f8b\u3002 \u6b64\u5916\uff0c\u5f53\u672a\u77e5\u6279\u6b21\u56e0\u5b50\u65f6\uff0c\u4e5f\u53ef\u4ee5\u5e94\u7528ARSyN\uff0c\u56e0\u4e3a\u5bf9\u6b8b\u5dee\u77e9\u9635\u8fdb\u884cPCA\u53ef\u4ee5\u68c0\u6d4b\u5230\u4e0e\u5b9e\u9a8c\u8bbe\u8ba1\u4e2d\u672a\u5305\u62ec\u7684\u53d8\u5f02\u6e90\u76f8\u5173\u7684\u5173\u8054\u7ed3\u6784\u3002\u5f53PCA\u7684\u7b2c\u4e00\u7279\u5f81\u503c\u660e\u663e\u9ad8\u4e8e\u5176\u4ed6\u7279\u5f81\u503c\u65f6\uff0c\u6211\u4eec\u4f1a\u6ce8\u610f\u5230\u6b8b\u5dee\u4e2d\u7684\u8fd9\u79cd\u4fe1\u53f7\uff0c\u56e0\u4e3a\u5982\u679c\u6ca1\u6709\u4efb\u4f55\u7ed3\u6784\uff0c\u7279\u5f81\u503c\u5927\u81f4\u76f8\u7b49\u3002\u5728\u8fd9\u79cd\u60c5\u51b5\u4e0b\uff0c\u7ec4\u4ef6\u7684\u9009\u62e9\u7531\u03b2\u53c2\u6570\u63a7\u5236\u3002\u8868\u793a\u7cfb\u7edf\u6027\u566a\u58f0\u5e76\u4ece\u539f\u59cb\u6570\u636e\u4e2d\u5220\u9664\u7684\u7ec4\u4ef6\u662f\u90a3\u4e9b\u4ee3\u8868\u5e73\u5747\u53d8\u5f02\u6027\u8d85\u8fc7\u03b2\u500d\u7684\u7ec4\u4ef6\u3002<\/span><\/span><\/p>\n<section style=\"font-size: 16px;margin-bottom: 0px;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(69, 107, 176);padding-right: 6px;padding-bottom: 6px;padding-left: 6px;\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;transform: translate3d(19px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"text-align: justify;color: rgb(255, 255, 255);\">\n <\/p>\n<\/section>\n<\/section>\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(255, 255, 255);padding: 23px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n\u516c\u4f17\u53f7\u540e\u53f0\u56de\u590d\u201c111\u201d<\/span>\u9886\u53d6\u672c\u7bc7\u4ee3\u7801\u3001\u57fa\u56e0\u96c6\u6216\u793a\u4f8b\u6570\u636e\u7b49\u6587\u4ef6\uff1b<\/p>\n\u6587\u4ef6\u7f16\u53f7\uff1a231210<\/strong><\/em><\/span><\/p>\n\u679c\u7c89\u798f\u5229<\/span><\/strong>\uff1a\u751f\u4fe1\u4eba\u5fc5\u5907\u795e\u5668\u2014\u2014\u670d\u52a1\u5668<\/strong><\/span> <\/p>\n\u5e73\u65f6\u751f\u4fe1\u5206\u6790\u5b66\u4e60\u4e2d\u6709\u8981\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u8054\u7cfb\u5c0f\u679c\u79df\u8d41\uff0c\u7c89\u4e1d\u798f\u5229\u90fd\u662f\u5e02\u573a\u8d85\u4f4e\u4ef7\u683c\uff0c\u8d76\u5feb\u627e\u5c0f\u679c\u9886\u53d6\u514d\u8d39\u7684\u8bd5\u7528\u8d26\u53f7\u5427\uff01<\/p>\n<a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247495825&idx=2&sn=a22a72496a1c082ea5b827be94ce4d99&chksm=cf7f6054f808e94264e14bfed4359cab3fcaaca249952a9f761c37ece352dcd7108579788b89&scene=21#wechat_redirect\" textvalue=\"\u670d\u52a1\u5668\u4ef7\u683c\u914d\u7f6e\u8868\uff08\u70b9\u51fb\u94fe\u63a5\u67e5\u770b\uff09\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" rel=\"noopener\">\u670d\u52a1\u5668\u4ef7\u683c\u914d\u7f6e\u8868\uff08\u70b9\u51fb\u94fe\u63a5\u67e5\u770b\uff09<\/a><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n\u793a\u4f8b\uff1a\u9175\u6bcd\u8868\u8fbe\u6570\u636e<\/strong><\/span><\/p>\n\u9175\u6bcd\u8868\u8fbe\u4f8b\u6570\u636e\u96c6\u4eceGene Expression Omnibus\uff08GEO\uff09\u6570\u636e\u5e93\u548c\u4e09\u4e2a\u4e0d\u540c\u7684\u5b9e\u9a8c\u5ba4\uff08\u6279\u6b21\uff09\u4e2d\u6536\u96c6\u3002\u5728\u6240\u6709\u8fd9\u4e9b\u6570\u636e\u96c6\u4e2d\uff0c\u5206\u6790\u4e86\u9175\u6bcd\u4e2d\u8461\u8404\u7cd6\u9965\u997f\u7684\u5f71\u54cd\u3002Lab A\u662fUniversitat de Valencia\u7684\u751f\u7269\u5316\u5b66\u548c\u5206\u5b50\u751f\u7269\u5b66\u90e8\u95e8\uff08\u5b58\u53d6\u53f7GSE11521\uff09[<\/span>2<\/span>]; Lab B\u662f\u54c8\u4f5b\u5927\u5b66\u7684\u5206\u5b50\u548c\u7ec6\u80de\u751f\u7269\u5b66\u90e8\u95e8\uff08\u5b58\u53d6\u53f7GSE56622\uff09[<\/span>5<\/span>]; \u548cLab C\u662f\u7ea6\u7ff0\u970d\u666e\u91d1\u65af\u5927\u5b66\u7684\u751f\u7269\u5b66\u90e8\u95e8\uff08\u5b58\u53d6\u53f7GSE43747\uff09[<\/span>6<\/span>]\u3002 \u5bf9\u4e8e\u6bcf\u4e2a\u75c5\u4f8b\u8fdb\u884c\u9002\u5f53\u7684\u6570\u636e\u9884\u5904\u7406\u540e\uff0c\u5fc5\u8981\u65f6\u5e94\u7528\u4e86voom\u8f6c\u6362\uff08\u4f7f\u7528limma R\u5305\uff09\u3002\u6700\u540e\uff0c\u5bf9\u6765\u81ea\u6240\u6709\u5b9e\u9a8c\u5ba4\u7684\u6240\u6709\u6837\u672c\u8fdb\u884c\u4e86TMM\u5f52\u4e00\u5316\u3002\u901a\u8fc7\u4ece\u6bcf\u4e2a\u6570\u636e\u77e9\u9635\u4e2d\u9009\u62e9200\u4e2a\u7ec4\u5b66\u53d8\u91cf\u5e76\u4ec5\u4eceA\u5b9e\u9a8c\u5ba4\u9009\u62e93\u4e2a\u6837\u672c\uff0c\u83b7\u5f97\u4e86\u51cf\u5c11\u7684\u6570\u636e\u96c6\u3002\u8fd9\u4e2a\u9175\u6bcd\u591a\u7ec4\u5b66\u51cf\u5c11\u7684\u6570\u636e\u96c6\u5305\u542b\u5728<\/span>MutiBaC<\/span>\u5305\u4e2d\uff0c\u7528\u4e8e\u8bf4\u660e\u8be5\u5305\u7684\u7528\u6cd5\u3002\u53ef\u4ee5\u4f7f\u7528<\/span>data(\u201cmultiyeast\u201d\uff09<\/span>\u6307\u4ee4\u52a0\u8f7d\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u3002 \u8fd9\u4e09\u9879\u7814\u7a76\u4f7f\u7528\u4e86\u76f8\u5f53\u7684\u9175\u6bcd\u83cc\u682a\u548c\u5b9e\u9a8c\u6761\u4ef6\uff0c\u4f46\u5982\u56fe1\u6240\u793a\uff0c\u5bf9\u8868\u8fbe\u7684\u4e3b\u8981\u5f71\u54cd\u662f\u7531\u4e8e\u5c5e\u4e8e\u4e0d\u540c\u5b9e\u9a8c\u5ba4\u7684\u6570\u636e\uff0c\u5373\u672c\u4f8b\u4e2d\u7684\u6279\u6b21\u3002 <img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014465\" data-ratio=\"0.5601851851851852\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_H9IkhYjUsxTsbjnCCdrqX5h4AB4eMQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSvXrLibRUlbBT315KFd6wibzBhqH9IkhYjUsxTsbjnCCdrqX5h4AB4eMQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"313.6000061035156\" width=\"560.010009765625\" \/> <\/span><\/span>\u56fe1\uff1a<\/span>\u539f\u59cb\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684\u4e3b\u6210\u5206\u5206\u6790\u56fe\uff08\u6821\u6b63\u524d\uff09<\/span>\u6279\u6b21\u4e4b\u95f4\u5b8c\u5168\u5206\u5f00\u3002\u4f7f\u7528MultiBaC\u5305\u751f\u6210\u7684\u56fe\uff08\u89c1\u7ed3\u679c\u53ef\u89c6\u5316\u90e8\u5206)\u3002<\/span> <\/span> <\/span><o:page><\/o:page><\/p>\nARSyNbac\u8f93\u5165\u6570\u636e<\/strong><\/span><\/p>\nMultiBaC<\/span>\u5305\u4f7f\u7528\u7684\u662f<\/span>MultiAssayExperiment<\/span>\u5bf9\u8c61\uff0c\u8fd9\u662fBioconductor\u4e3a\u591a\u7ec4\u5b66\u7814\u7a76\u63d0\u4f9b\u7684\u4e00\u79cd\u5bb9\u5668\u7c7b\u578b\uff0c\u53ef\u4ee5\u4ece\u4e00\u4e2a\u7531\u77e9\u9635\u6216<\/span>data.frame<\/span>\u5bf9\u8c61\u7ec4\u6210\u7684\u5217\u8868\u4e2d\u521b\u5efa\u51fa\u6765\u3002\u8fd9\u4e9b\u77e9\u9635\u5fc5\u987b\u5177\u6709\u4ee5\u884c\u4e3a\u7279\u5f81\u3001\u4ee5\u5217\u4e3a\u6837\u54c1\u7684\u5e03\u5c40\uff0c\u5982\u4e0b\u9762\u6240\u793a\u7684\u9175\u6bcd\u793a\u4f8b\u6570\u636e\u77e9\u9635\u4e4b\u4e00(A.rna)\u3002\u91cd\u8981\u7684\u662f\uff0c\u6240\u6709\u6570\u636e\u77e9\u9635\u90fd\u5e94\u5177\u6709\u76f8\u540c\u7684\u53d8\u91cf\u7a7a\u95f4\u3002\u5982\u679c\u5404\u7ec4\u5b66\u7684\u53d8\u91cf\u6570\u91cf\u548c\u987a\u5e8f\u4e0d\u4e00\u81f4\uff0c\u90a3\u4e48<\/span>createMbac<\/span>\u51fd\u6570\u5c06\u4f1a\u9009\u62e9\u5171\u6709\u7684\u53d8\u91cf\u3002\u56e0\u6b64\uff0c\u6240\u6709\u884c\u5fc5\u987b\u4f7f\u7528\u540c\u7c7b\u578b\u7684\u6807\u8bc6\u7b26\u8fdb\u884c\u547d\u540d\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"css\"><code>data<\/span>(\"multiyeast<\/span>\") <\/span><\/code><code>head<\/span>(A<\/span>.rna<\/span>) <\/span><\/code><code>## A<\/span>.rna_Glu<\/span>+_1 A<\/span>.rna_Glu<\/span>+_2 A<\/span>.rna_Glu<\/span>+_3 A<\/span>.rna_Glu-_1<\/span> A<\/span>.rna_Glu-_2<\/span> <\/span><\/code><code>## YOR324C<\/span> 7.174264<\/span> 6.976815<\/span> 7.482661<\/span> 8.020596<\/span> 7.736636<\/span> <\/span><\/code><code>## YGL104C<\/span> 4.239493<\/span> 4.284775<\/span> 3.100898<\/span> 4.957403<\/span> 3.673252<\/span> <\/span><\/code><code>## YOR142W<\/span> 8.819824<\/span> 8.496966<\/span> 9.026971<\/span> 10.374525<\/span> 10.294006<\/span> <\/span><\/code><code>## YOR052C<\/span> 6.721211<\/span> 7.011932<\/span> 7.557519<\/span> 8.504503<\/span> 8.586738<\/span> <\/span><\/code><code>## YGR038W<\/span> 5.878483<\/span> 5.894121<\/span> 6.468361<\/span> 7.856822<\/span> 7.806318<\/span> <\/span><\/code><code>## YER087W<\/span> 5.131089<\/span> 5.295029<\/span> 5.750657<\/span> 2.920250<\/span> 5.496136<\/span> <\/span><\/code><code>## A<\/span>.rna_Glu-_3<\/span> <\/span><\/code><code>## YOR324C<\/span> 7.922425<\/span> <\/span><\/code><code>## YGL104C<\/span> 1.587184<\/span> <\/span><\/code><code>## YOR142W<\/span> 10.979224<\/span> <\/span><\/code><code>## YOR052C<\/span> 8.221168<\/span> <\/span><\/code><code>## YGR038W<\/span> 8.108436<\/span> <\/span><\/code><code>## YER087W<\/span> 2.879254<\/span><\/span><\/code><\/pre>\n<\/section>\n\u5bf9\u4e8e\u6bcf\u4e2a\u6279\u6b21\uff08\u672c\u4f8b\u4e2d\u7684\u5b9e\u9a8c\u5ba4\uff09\uff0c\u9700\u8981\u521b\u5efa\u4e00\u4e2a\u201cMultiAssayExperiment\u201d\u5bf9\u8c61\u3002\u65b0\u7684\u6570\u636e\u7ed3\u6784\u201cmbac\u201d\u662f\u4e00\u4e2a\u201cMultiAssayExperiment\u201d\u5bf9\u8c61\u7684\u5217\u8868\uff0c\u53ef\u4ee5\u4f7f\u7528\u5305\u4e2d\u7684\u201ccreateMbac\u201d\u51fd\u6570\u8f7b\u677e\u751f\u6210\u3002\u751f\u6210\u7684\u201cmbac\u201d\u5bf9\u8c61\u5c06\u662f\u201cARSyNbac\u201d\u7684\u8f93\u5165\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"swift\"><code>data_RNA<-createMbac (inputOmics =list(A<\/span>.rna, B<\/span>.rna, C<\/span>.rna), <\/span><\/code><code> batchFactor =c<\/span>(\"A\"<\/span>, \"B\"<\/span>, \"C\"<\/span>), <\/span><\/code><code> experimentalDesign =list(\"A\"<\/span>= c<\/span>(\"Glu+\"<\/span>, \"Glu+\"<\/span>, <\/span><\/code><code> \"Glu+\"<\/span>, \"Glu-\"<\/span>, <\/span><\/code><code> \"Glu-\"<\/span>, \"Glu-\"<\/span>), <\/span><\/code><code> \"B\"<\/span>=c<\/span>(\"Glu+\"<\/span>, \"Glu+\"<\/span>, <\/span><\/code><code> \"Glu-\"<\/span>, \"Glu-\"<\/span>), <\/span><\/code><code> \"C\"<\/span>=c<\/span>(\"Glu+\"<\/span>, \"Glu+\"<\/span>, <\/span><\/code><code> \"Glu-\"<\/span>, \"Glu-\"<\/span>)), <\/span><\/code><code> omicNames =\"RNA\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n\u4ee5\u4e0b\u662f<\/span>createMbac<\/span>\u51fd\u6570\u53c2\u6570\u7684\u8bf4\u660e\uff1a<\/span><\/span><\/p>\n\u2022<\/span>inputOmics<\/span> \u5305\u542b\u8981\u5206\u6790\u7684\u6240\u6709\u77e9\u9635\u6216\u6570\u636e\u6846\u5bf9\u8c61\u7684\u5217\u8868\u3002\u4e5f\u53ef\u4ee5\u63d0\u4f9b MultiAssayExperiment \u5bf9\u8c61\u3002<\/span><\/span><\/p>\n\u2022<\/span>batchFactor<\/span> \u4e00\u4e2a\u5411\u91cf\u6216\u56e0\u5b50\uff0c\u6307\u793a\u6bcf\u4e2a\u8f93\u5165\u77e9\u9635\u6240\u5c5e\u7684\u6279\u6b21\uff08\u5373\u7814\u7a76\u3001\u5b9e\u9a8c\u5ba4\u3001\u65f6\u95f4\u70b9\u7b49\uff09\u3002\u5982\u679c\u4e3a NULL\uff08\u9ed8\u8ba4\u503c\uff09\uff0c\u5219\u4e0d\u8003\u8651\u6279\u6b21\uff0c\u53ea\u53ef\u4f7f\u7528 ARSyNbac \u566a\u58f0\u51cf\u5c11\u6a21\u5f0f\u3002<\/span><\/span><\/p>\n\u2022<\/span>experimentalDesign<\/span> \u5305\u542b\u4e0e\u6279\u6b21\u6570\u91cf\u76f8\u540c\u7684\u5143\u7d20\u7684\u5217\u8868\u3002\u6bcf\u4e2a\u5143\u7d20\u53ef\u4ee5\u662f\u56e0\u5b50\u3001\u5b57\u7b26\u5411\u91cf\u6216\u6570\u636e\u6846\uff0c\u8868\u793a\u8be5\u6279\u6b21\u4e2d\u6bcf\u4e2a\u6837\u672c\u7684\u5b9e\u9a8c\u6761\u4ef6\u3002\u5f53\u662f\u5177\u6709\u591a\u5217\uff08\u591a\u56e0\u7d20\u5b9e\u9a8c\u8bbe\u8ba1\uff09\u7684\u6570\u636e\u6846\u65f6\uff0c\u4e0d\u540c\u5217\u5c06\u7ec4\u5408\u6210\u4e00\u4e2a\u5355\u4e00\u5217\uff0c\u7531 MultiBaC \u6216 ARSyNbac \u4f7f\u7528\u3002\u5728\u4efb\u4f55\u60c5\u51b5\u4e0b\uff0c\u5b9e\u9a8c\u8bbe\u7f6e\u5fc5\u987b\u5bf9\u6240\u6709\u6279\u6b21\u76f8\u540c\u3002\u6b64\u5916\uff0c\u6b64\u5217\u8868\u4e2d\u5143\u7d20\u7684\u540d\u5b57\u5fc5\u987b\u4e0e <\/span>batches<\/span> \u53c2\u6570\u4e2d\u58f0\u660e\u7684\u540d\u5b57\u76f8\u540c\u3002\u5982\u679c\u4e0d\u76f8\u540c\uff08\u6216\u4e3a NULL\uff09\uff0c\u5219\u5f3a\u5236\u5c06\u540d\u79f0\u4e0e <\/span>batches<\/span> \u53c2\u6570\u4e2d\u7684\u540d\u79f0\u76f8\u540c\u5e76\u6309\u76f8\u540c\u987a\u5e8f\u6392\u5217\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n\u2022<\/span>omicNames<\/span> \u6bcf\u4e2a\u8f93\u5165\u77e9\u9635\u7684\u540d\u79f0\u5411\u91cf\u3002\u8981\u6c42\u5171\u6709\u7684 omic \u5728\u6240\u6709\u6279\u6b21\u4e2d\u5177\u6709\u76f8\u540c\u7684\u540d\u79f0\u3002<\/span><\/span><\/p>\n\u2022<\/span>commonOmic<\/span> \u6279\u6b21\u4e4b\u95f4\u5171\u6709\u7684 omic \u7684\u540d\u79f0\u3002\u5fc5\u987b\u662f omicNames \u53c2\u6570\u4e2d\u7684\u4e00\u4e2a\u540d\u79f0\u3002\u5982\u679c\u4e3a NULL\uff08\u9ed8\u8ba4\u503c\uff09\uff0c\u5c06\u9009\u62e9\u6240\u6709\u6279\u6b21\u4e2d\u5171\u6709\u7684 omic \u540d\u79f0\u4f5c\u4e3a commonOmic\u3002 \u7531createMbac\u51fd\u6570\u751f\u6210\u7684mbac R\u7ed3\u6784\u662f\u4e00\u4e2aS3\u5bf9\u8c61\uff0c\u6700\u521d\u53ea\u5305\u542b\u4e00\u4e2a\u69fd\uff0c\u5373ListOfBatches\u5bf9\u8c61\u3002\u5f53\u8fd0\u884cARSyNbac\u6216MultiBaC\u51fd\u6570\u65f6\uff0c\u968f\u7740\u5b83\u4eec\u88ab\u521b\u5efa\uff0c\u8fd9\u4e2ambac\u7ed3\u6784\u5c06\u5305\u542b\u66f4\u591a\u7684\u5143\u7d20\u3002\u8fd9\u4e9b\u65b0\u69fd\u662fCorrectedData\u3001PLSmodels\u3001ARSyNmodels\u6216InnerRelation\uff0c\u4e0b\u9762\u8fdb\u884c\u63cf\u8ff0\uff1a<\/span><\/span><\/p>\n\u2022<\/span>ListOfBatches<\/span>: \u4e00\u4e2a\u5305\u542b\u591a\u4e2aMultiAssayExperiment\u5bf9\u8c61\u7684\u5217\u8868\uff08\u6bcf\u4e2a\u6279\u6b21\u4e00\u4e2a\u5bf9\u8c61\uff09\u3002<\/span><\/span><\/p>\n\u2022<\/span>CorrectedData<\/span>: \u4e0eListOfBatches\u7ed3\u6784\u76f8\u540c\uff0c\u4f46\u662f\u5305\u542b\u4fee\u6b63\u540e\u7684\u6570\u636e\u77e9\u9635\uff0c\u800c\u4e0d\u662f\u539f\u59cb\u77e9\u9635\u3002<\/span><\/span><\/p>\n\u2022<\/span>PLSmodels<\/span>: \u7531MultiBaC\u65b9\u6cd5\u521b\u5efa\u7684PLS\u6a21\u578b\uff08\u6bcf\u4e2a\u975e\u516c\u5171omic\u6570\u636e\u7c7b\u578b\u4e00\u4e2a\u6a21\u578b\uff09\u3002\u4ec5\u9002\u7528\u4e8eMultiBaC\u65b9\u6cd5\u3002<\/span><\/span><\/p>\n\u2022<\/span>ARSyNmodels<\/span>: \u7531ARSyNbac\u6216MultiBaC\u51fd\u6570\u521b\u5efa\u7684ARSyN\u6a21\u578b\u3002<\/span><\/span><\/p>\n\u2022<\/span>InnerRelation<\/span>: \u4e00\u4e2a\u7c7b\u4e3a<\/span>data.frame<\/span>\u7684\u8868\uff0c\u5305\u542b\u6bcf\u4e2aPLS\u6a21\u578b\u5728\u6240\u6709\u7ec4\u4ef6\u95f4\u7684\u5185\u90e8\u76f8\u5173\u6027\uff08\u5373X\uff08t\uff09\u548cY\uff08u\uff09\u77e9\u9635\u5f97\u5206\u95f4\u7684\u76f8\u5173\u6027\uff09\uff0c\u7528\u4e8e\u6a21\u578b\u9a8c\u8bc1\u3002\u4ec5\u9002\u7528\u4e8eMultiBaC\u65b9\u6cd5\u3002<\/span><\/span><\/p>\n\u2022<\/span>commonOmic<\/span>: \u6279\u6b21\u95f4\u516c\u5171omic\u7684\u540d\u79f0\u3002 \u9664\u4e86\u7ed8\u56fe\u4e4b\u5916\uff0c\u8fd8\u63d0\u4f9b\u4e86\u7528\u4e8e\u53ef\u89c6\u5316mbac\u5bf9\u8c61\u7684\u5176\u4ed6\u65b9\u6cd5\uff1a\u6458\u8981\uff0c\u5b83\u663e\u793a\u4e86\u5bf9\u8c61\u7684\u7ed3\u6784\u3002<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code>summary(data_RNA) <\/span><\/code><code>#<\/span># [1] \"Object of class mbac: It contains 3 different bacthes and 1 omic type(s).\"<\/span><\/span><\/code><\/pre>\n<\/section>\n<table border=\"1\" cellspacing=\"0\" cellpadding=\"0\" style=\"margin-left: 0px;border-width: initial;border-style: none;border-color: initial;border-collapse: collapse;width: 100%;\">\n<thead>\n<tr>\n<td width=\"264\" valign=\"top\" style=\"border-width: initial;border-style: none;border-color: initial;padding: 0pt 5.4pt;word-break: break-all;\">\n <o:p> <\/o:p><\/span><\/p>\n<\/td>\n<td width=\"264\" valign=\"top\" style=\"border-top:none;border-left:none;border-bottom:none;border-right:none;padding:0pt 5.4pt 0pt 5.4pt;\">\nRNA<\/span><\/p>\n<\/td>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td width=\"264\" valign=\"top\" style=\"border-top:none;border-left:none;border-bottom:none;border-right:none;padding:0pt 5.4pt 0pt 5.4pt;\">\nA<\/span><\/p>\n<\/td>\n<td width=\"264\" valign=\"top\" style=\"border-top:none;border-left:none;border-bottom:none;border-right:none;padding:0pt 5.4pt 0pt 5.4pt;\">\nTrue<\/span><\/p>\n<\/td>\n<\/tr>\n<tr>\n<td width=\"264\" valign=\"top\" style=\"border-top:none;border-left:none;border-bottom:none;border-right:none;padding:0pt 5.4pt 0pt 5.4pt;\">\nB<\/span> <\/span><o:page><\/o:page><\/p>\n<\/td>\n<td width=\"264\" valign=\"top\" style=\"border-top:none;border-left:none;border-bottom:none;border-right:none;padding:0pt 5.4pt 0pt 5.4pt;\">\nTrue<\/span><\/p>\n<\/td>\n<\/tr>\n<tr>\n<td width=\"264\" valign=\"top\" style=\"border-top:none;border-left:none;border-bottom:none;border-right:none;padding:0pt 5.4pt 0pt 5.4pt;\">\nC<\/span><\/p>\n<\/td>\n<td width=\"264\" valign=\"top\" style=\"border-top:none;border-left:none;border-bottom:none;border-right:none;padding:0pt 5.4pt 0pt 5.4pt;\">\nTrue<\/span><\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100014488\" data-ratio=\"0.38981481481481484\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_IWicymEetCc6Enf2BkUE4Yz1Ya5e5w-2.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyuYsqlJnQUJvnS2iciaDibtfbdV0VmHlriaSjYwjFPLp1BLjokHIWicymEetCc6Enf2BkUE4Yz1Ya5e5w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"letter-spacing: 0.578px;text-wrap: wrap;color: rgb(34, 34, 38);font-family: "Times New Roman";font-size: 15px;font-weight: 700;background-color: rgb(255, 255, 255);text-align: center;\" \/>ARSyNbac\u6821\u6b63<\/strong><\/span><\/p>\nMultiBaC<\/span>\u5305\u4e2d\u7528\u4e8e\u4ece\u5355\u4e00\u6837\u672c\u6570\u636e\u77e9\u9635\u4e2d\u53bb\u9664\u6279\u6b21\u6548\u5e94\u6216\u4e0d\u9700\u8981\u7684\u566a\u58f0\u7684\u51fd\u6570\u662f<\/span>ARSyNbac<\/span>\u51fd\u6570\uff0c\u5b83\u5141\u8bb8\u4ee5\u4e0b\u53c2\u6570\uff1a<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code>ARSyNbac (mbac, batchEstimation = TRUE<\/span>, filterNoise = TRUE<\/span>, <\/span><\/code><code> Interaction=FALSE<\/span>, Variability = 0.90<\/span>, beta = 2<\/span>, <\/span><\/code><code> modelName = \"Model 1\"<\/span>, <\/span><\/code><code> showplot = TRUE<\/span>)<\/span><\/code><\/pre>\n<\/section>\n\u2022<\/span>mbac<\/span>: \u901a\u8fc7 <\/span>createMbac<\/span> \u751f\u6210\u7684 mbac \u5bf9\u8c61\u3002<\/span><\/span><\/p>\n\u2022<\/span>batchEstimation<\/span>: \u903b\u8f91\u503c\u3002\u5982\u679c\u4e3a TRUE\uff08\u9ed8\u8ba4\u503c\uff09\uff0c\u5219\u4f30\u7b97\u6279\u6b21\u6548\u5e94\u5e76\u7528\u4e8e\u6821\u6b63\u6570\u636e\u3002\u5f53\u5df2\u77e5\u6279\u6b21\u6548\u5e94\u7684\u6765\u6e90\u65f6\uff0c\u8bf7\u4f7f\u7528 TRUE\u3002<\/span><\/span><\/p>\n\u2022<\/span>filterNoise<\/span>: \u903b\u8f91\u503c\u3002\u5982\u679c\u4e3a TRUE\uff08\u9ed8\u8ba4\u503c\uff09\uff0c\u5219\u4ece\u6b8b\u5dee\u4e2d\u79fb\u9664\u7ed3\u6784\u5316\u566a\u58f0\u3002\u5f53\u6570\u636e\u4e2d\u5b58\u5728\u672a\u77e5\u6279\u6b21\u6548\u5e94\u6765\u6e90\u65f6\uff0c\u8bf7\u4f7f\u7528\u6b64\u9009\u9879\u3002<\/span><\/span><\/p>\n\u2022<\/span>Interaction<\/span>: \u903b\u8f91\u503c\u3002\u662f\u5426\u5efa\u7acb\u56e0\u7d20\u4e4b\u95f4\u7684\u4ea4\u4e92\u6a21\u578b\uff08\u9ed8\u8ba4\u4e3a FALSE\uff09\u3002<\/span><\/span><\/p>\n\u2022<\/span>Variability<\/span>: \u4ece 0 \u5230 1 \u7684\u503c\u3002\u6bcf\u4e2a\u6a21\u578b\u5fc5\u987b\u89e3\u91ca\u7684\u6570\u636e\u53d8\u5f02\u6027\u7684\u6700\u5c0f\u767e\u5206\u6bd4\u3002\u5728\u6279\u6b21\u6821\u6b63\u6a21\u5f0f\u4e0b\u4f7f\u7528\u3002\u9ed8\u8ba4\u503c\u4e3a 0.90\u3002<\/span><\/span><\/p>\n\u2022<\/span>beta<\/span>: \u6570\u503c\u3002\u8868\u793a\u8d85\u8fc7\u5e73\u5747\u53d8\u5f02\u6027\u7684 beta \u500d\u7684\u7ec4\u4ef6\u88ab\u786e\u5b9a\u4e3a\u6b8b\u5dee\u4e2d\u7684\u7cfb\u7edf\u566a\u58f0\u3002\u5728\u566a\u58f0\u51cf\u5c11\u6a21\u5f0f\u4e0b\u4f7f\u7528\u3002\u9ed8\u8ba4\u503c\u4e3a 2\u3002<\/span><\/span><\/p>\n\u2022<\/span>modelName<\/span>: \u521b\u5efa\u7684\u6a21\u578b\u7684\u540d\u79f0\u3002\u5982\u679c\u60a8\u4f7f\u7528 explaine_var \u7ed8\u56fe\u51fd\u6570\uff0c\u5219\u4f1a\u663e\u793a\u6b64\u540d\u79f0\u3002\u9ed8\u8ba4\u503c\u4e3a \u201cModel 1\u201d\u3002<\/span><\/span><\/p>\n\u2022<\/span>showplot<\/span>: \u903b\u8f91\u503c\u3002\u5982\u679c\u4e3a TRUE\uff08\u9ed8\u8ba4\u503c\uff09\uff0c\u5219\u663e\u793a explained_var \u7ed8\u56fe\u3002\u6b64\u7ed8\u56fe\u8868\u793a ARSyN \u6a21\u578b\u9009\u62e9\u7684\u7ec4\u4ef6\u6570\u91cf\u3002 \u56e0\u6b64\uff0c<\/span>ARSyNbac\u51fd\u6570\u63d0\u4f9b\u4e86\u4e09\u79cd\u5206\u6790\u7c7b\u578b\uff1a\u5f53\u63d0\u4f9b\u6279\u6b21\u4fe1\u606f\u65f6\u8fdb\u884c<\/span>ARSyNbac\u6279\u6b21\u6548\u5e94\u6821\u6b63<\/span>\uff0c\u5f53\u6279\u6b21\u4fe1\u606f\u672a\u77e5\u65f6\u8fdb\u884c<\/span>ARSyNbac\u566a\u58f0\u6291\u5236<\/span>\uff0c\u5f53\u5b58\u5728\u5df2\u77e5\u6279\u6b21\u6548\u5e94\u6e90\u548c\u53e6\u4e00\u4e2a\u53ef\u80fd\u7684\u672a\u77e5\u4e0d\u9700\u8981\u7684\u53ef\u53d8\u6027\u6e90\u65f6\u8fdb\u884c\u4e24\u8005\u7684\u7ec4\u5408\u6a21\u5f0f\u3002\u4ee5\u4e0b\u90e8\u5206\u8bf4\u660e\u5982\u4f55\u8fdb\u884c\u6bcf\u4e00\u79cd\u5206\u6790\u3002<\/span> <\/span><o:page><\/o:page><\/p>\nARSyNbac\u6279\u91cf\u6548\u5e94\u6821\u6b63<\/strong><\/span><\/p>\n\u5f53\u5728<\/span>mbac<\/span>\u8f93\u5165\u5bf9\u8c61\u7684<\/span>batchFactor<\/span>\u53c2\u6570\u4e2d\u6307\u5b9a\u6279\u6b21\u65f6\uff0c\u53ef\u4ee5\u901a\u8fc7\u9009\u62e9<\/span>batchEstimation = TRUE<\/span>\uff08\u4ec5\u8003\u8651\u4e00\u4e2a\u6279\u6b21\u6548\u5e94\u6e90\uff0c<\/span>filterNoise = FALSE<\/span>\uff09\u6765\u4f30\u8ba1\u5e76\u6d88\u9664\u5176\u5f71\u54cd\u3002\u6b64\u5916\uff0c\u901a\u8fc7\u8bbe\u7f6e<\/span>Interaction=TRUE<\/span>\u53ef\u4ee5\u7814\u7a76\u5b9e\u9a8c\u56e0\u7d20\u4e0e\u6279\u6b21\u56e0\u7d20\u4e4b\u95f4\u7684\u76f8\u4e92\u4f5c\u7528\u3002<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code>par(mfrow = c(1<\/span>,2<\/span>)) <\/span><\/code><code>arsyn_1 <- ARSyNbac(data_RNA, modelName = \"RNA\"<\/span>, Variability = 0.95<\/span>, <\/span><\/code><code> batchEstimation = TRUE<\/span>, filterNoise = FALSE<\/span>, Interaction = FALSE<\/span>) <\/span><\/code><code>plot(arsyn_1, typeP=\"pca.cor\"<\/span>, bty = \"L\"<\/span>, <\/span><\/code><code> pch = custom_pch, cex = 3<\/span>, col.per.group = custom_col, <\/span><\/code><code> legend.text = c(\"Color: Batch\"<\/span>, names(data_RNA$ListOfBatches), <\/span><\/code><code> \"Fill: Cond.\"<\/span>, unique(colData(data_RNA$ListOfBatches$A)$tfactor)), <\/span><\/code><code> args.legend = list<\/span>(\"x\"<\/span> = \"topright\"<\/span>, <\/span><\/code><code> \"pch\"<\/span> = c(NA, 15<\/span>, 15<\/span>, 15<\/span>, <\/span><\/code><code> NA, 15<\/span>, 0<\/span>), <\/span><\/code><code> \"col\"<\/span> = c(NA, \"brown2\"<\/span>, \"dodgerblue\"<\/span>, \"forestgreen\"<\/span>, <\/span><\/code><code> NA, 1<\/span>, 1<\/span>), <\/span><\/code><code> \"bty\"<\/span> = \"n\"<\/span>, <\/span><\/code><code> \"cex\"<\/span> = 1.2<\/span>))<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014467\" data-ratio=\"0.5574074074074075\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_gvuSTbB5M5OVH38Dnvj2z4DE4iaE6g.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSc1nbCcYcp9E6zuovWsWBKLTxqgvuSTbB5M5OVH38Dnvj2z4DE4iaE6g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"312.0\" width=\"560.010009765625\" \/><\/span> <\/span>\u56fe2\uff1a<\/span>\u4e0d\u8003\u8651\u4ea4\u4e92\u4f5c\u7528\u6279\u5904\u7406\u65f6\u7684\u6279\u6b21\u6821\u6b63<\/span><\/span><\/p>\n\u5de6\u56fe\uff1a\u89e3\u91ca\u65b9\u5dee\u56fe\u3002\u5f53showplot=TRUE\u65f6\u663e\u793a\u9ed8\u8ba4\u56fe\u5f62\u3002\u8be5\u56fe\u8868\u793a\u4e3a\u89e3\u91ca\u611f\u5174\u8da3\u6548\u5e94\uff08\u6279\u6b21\u6548\u5e94\uff09\u7684\u67d0\u79cd\u53d8\u5f02\u6027\uff08y\u8f74\uff09\u6240\u9700\u7684\u7ec4\u5206\u6570\u91cf\uff08x\u8f74\uff09\u3002\u6a21\u578b\u9009\u62e9\u7684\u7ec4\u5206\u6570\u91cf\u7528\u4e09\u89d2\u5f62\u7b26\u53f7\u8868\u793a\u3002\u7070\u8272\u7684\u865a\u7ebf\u8868\u793a\u7531Variability\u53c2\u6570\u7ed9\u51fa\u7684\u9608\u503c\uff08\u767e\u5206\u6bd4\uff09\u3002\u53f3\u56fe\uff1a\u4e0d\u8003\u8651\u6279\u6b21\u548c\u6761\u4ef6\u4e4b\u95f4\u7684\u4ea4\u4e92\u4f5c\u7528\u65f6\uff0c\u7ecf\u8fc7\u6821\u6b63\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684PCA\u56fe\u3002 <\/span> \u6839\u636e\u56fe2\u7684\u5de6\u56fe\uff0c\u5df2\u9009\u62e9\u4e24\u4e2a\u4e3b\u6210\u5206\uff08PCs\uff09\u6765\u89e3\u91ca\u6279\u6b21\u6548\u5e94\u603b\u53d8\u5f02\u7684\u81f3\u5c1195%\u3002\u53f3\u56fe\u663e\u793a\u4e86\u4f7f\u7528\u8fd9\u79cd\u5206\u6790\u5bf9\u4fee\u6b63\u540e\u7684\u6570\u636e\u8fdb\u884cPCA\u3002\u73b0\u5728\u6570\u636e\u4e2d\u7684\u4e3b\u8981\u53d8\u5f02\u6e90\uff08PC1)\u7531\u5b9e\u9a8c\u6761\u4ef6\u51b3\u5b9a\uff0c\u800c\u6837\u672c\u4e0d\u518d\u6309\u6279\u6b21\u805a\u7c7b\u3002<\/span><\/span> <\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code>par(mfrow =c(1<\/span>,2<\/span>)) <\/span><\/code><code>arsyn_2 <-ARSyNbac(data_RNA, modelName =\"RNA\"<\/span>, Variability =0.95<\/span>, <\/span><\/code><code> batchEstimation =TRUE<\/span>, filterNoise =FALSE<\/span>, Interaction =TRUE<\/span>) <\/span><\/code><code>plot(arsyn_2, typeP=\"pca.cor\"<\/span>, bty =\"L\"<\/span>, <\/span><\/code><code> pch = custom_pch, cex =3<\/span>, col.per.group = custom_col, <\/span><\/code><code> legend.text =c(\"Color: Batch\"<\/span>, names(data_RNA$ListOfBatches), <\/span><\/code><code> \"Fill: Cond.\"<\/span>, unique(colData(data_RNA$ListOfBatches$A)$tfactor)), <\/span><\/code><code> args.legend =list<\/span>(\"x\"<\/span>=\"topright\"<\/span>, <\/span><\/code><code> \"pch\"<\/span>=c(NA, 15<\/span>, 15<\/span>, 15<\/span>, <\/span><\/code><code> NA, 15<\/span>, 0<\/span>), <\/span><\/code><code> \"col\"<\/span>=c(NA, \"brown2\"<\/span>, \"dodgerblue\"<\/span>, \"forestgreen\"<\/span>, <\/span><\/code><code> NA, 1<\/span>, 1<\/span>), <\/span><\/code><code> \"bty\"<\/span>=\"n\"<\/span>, <\/span><\/code><code> \"cex\"<\/span>=1.2<\/span>))<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" loading=\"lazy\" data-imgfileid=\"100014468\" data-ratio=\"0.5611111111111111\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_9aJMHw2RaqO0xYl0MLnicgxQgpk1sg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSIgiadnPnKkHibsAeJvcU7ibqnNOf9aJMHw2RaqO0xYl0MLnicgxQgpk1sg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"314.0000305175781\" width=\"560.010009765625\" class=\"rich_pages wxw-img\" \/><\/span> <\/span>\u56fe3\uff1a<\/span>\u4ea4\u4e92\u4f5c\u7528=TRUE\u65f6\u7684\u6279\u6b21\u6821\u6b63<\/span><\/span><\/p>\n\u5de6\u56fe\uff1a\u65b9\u5dee\u89e3\u91ca\u56fe\u3002\u5f53showplot=TRUE\u65f6\uff0c\u9ed8\u8ba4\u663e\u793a\u6b64\u56fe\u3002\u8be5\u56fe\u8868\u793a\u4e3a\u4e86\u89e3\u91ca\u611f\u5174\u8da3\u7684\u6548\u5e94\uff08\u6279\u6b21\u6548\u5e94\uff09\u7684\u67d0\u4e00\u90e8\u5206\uff08y\u8f74\uff09\u6240\u9700\u7684\u7ec4\u5206\u6570\u91cf\uff08x\u8f74\uff09\u3002\u6a21\u578b\u4e2d\u6240\u9009\u62e9\u7684\u7ec4\u5206\u6570\u91cf\u7528\u4e09\u89d2\u5f62\u7b26\u53f7\u8868\u793a\u3002\u7070\u8272\u7684\u865a\u7ebf\u8868\u793a\u7531Variability\u53c2\u6570\uff08\u4ee5\u767e\u5206\u6bd4\u5f62\u5f0f\uff09\u7ed9\u51fa\u7684\u9608\u503c\u3002 \u53f3\u56fe\uff1a\u7ecf\u8fc7\u6279\u6b21\u6761\u4ef6\u4ea4\u4e92\u6821\u6b63\u540e\u7684\u57fa\u56e0\u8868\u8fbePCA\u56fe\u8c31\u3002 \u5728\u56fe3\uff08\u53f3\u4fa7\u9762\u677f\uff09\u4e2d\uff0cPC1\u4e3a\u8d1f\u7684\u6240\u6709\u70b9\u90fd\u5bf9\u5e94\u4e8eGlu-\u6837\u672c\uff0c\u800cPC1\u4e3a\u6b63\u7684\u6240\u6709\u70b9\u5bf9\u5e94\u4e8eGlu+\u6837\u672c\uff0c\u6b63\u5982\u5728\u6a21\u578b\u4e2d\u4e0d\u5305\u62ec\u76f8\u4e92\u4f5c\u7528\u65f6\u6240\u53d1\u751f\u7684\u60c5\u51b5\u4e00\u6837\uff08\u56fe2\uff0c\u53f3\u4fa7\u9762\u677f\uff09\u3002\u7136\u800c\uff0c\u5728\u6b64\u7b2c\u4e8c\u6a21\u578b\u4e2d\uff0cPC1\u5bf9\u6570\u636e\u53d8\u5f02\u6027\u7684\u89e3\u91ca\u767e\u5206\u6bd4\u66f4\u9ad8\uff0c\u8868\u660e\u6279\u6b21\u6548\u5e94\u6821\u6b63\u6548\u679c\u66f4\u597d\u3002\u4e00\u822c\u6765\u8bf4\uff0c\u6211\u4eec\u5efa\u8bae\u4f7f\u7528\u9ed8\u8ba4\u53c2\u6570\uff08Interaction=FALSE)\uff0c\u56e0\u4e3a\u5c06\u90e8\u5206\u4fe1\u53f7\u89c6\u4e3a\u6279\u6b21\u6548\u5e94\u53ef\u80fd\u5bfc\u81f4\u6240\u9700\u4fe1\u53f7\u7684\u6548\u679c\u88ab\u7a00\u91ca\u3002\u4f46\u662f\uff0c\u6279\u6b21\u548c\u5b9e\u9a8c\u6761\u4ef6\u4e4b\u95f4\u7684\u76f8\u4e92\u4f5c\u7528\u6709\u65f6\u53ef\u80fd\u5f88\u5f3a\u70c8\uff0c\u56e0\u6b64\u6211\u4eec\u5e94\u8be5\u8003\u8651\u5c06\u76f8\u4e92\u4f5c\u7528\u5305\u62ec\u5728\u6a21\u578b\u4e2d\uff0c\u4ee5\u66f4\u597d\u5730\u6821\u6b63\u6570\u636e\u3002 \u56fe1\u3001\u56fe2\u548c\u56fe3\u4e2d\u7684PCA\u56fe\u662f\u7531MultiBaC\u5305\u4e2d\u7684\u81ea\u5b9a\u4e49plot\u51fd\u6570\u751f\u6210\u7684\u3002\u6709\u5173\u6b64\u51fd\u6570\u7684\u66f4\u591a\u8be6\u7ec6\u4fe1\u606f\uff0c\u8bf7\u5728\u201cARSyN\u548cMultiBaC\u7ed3\u679c\u7684\u89c6\u89c9\u5448\u73b0\u201d\u90e8\u5206\u67e5\u627e\uff0c\u5176\u4e2d\u5b8c\u6574\u63cf\u8ff0\u4e86plot\u51fd\u6570\u7684\u6240\u6709\u53c2\u6570\u3002<\/span> <\/span><o:page><\/o:page><\/p>\nARSyNbac\u53bb\u566a<\/strong><\/span><\/p>\n\u5f53batch\u672a\u88ab\u8bc6\u522b\u65f6\uff0c<\/span>ARSyNbac<\/span>\u901a\u8fc7\u8bbe\u7f6e<\/span>batchEstimation = FALSE<\/span>\u548c<\/span>filterNoise = TRUE<\/span>\u5bf9\u6b8b\u5dee\u4e2d\u7cfb\u7edf\u566a\u58f0\u7684\u5b58\u5728\u8fdb\u884c\u5206\u6790\u3002<\/span><\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code>par(mfrow =c(1<\/span>,2<\/span>)) <\/span><\/code><code>arsyn_3 <-ARSyNbac(data_RNA, modelName =\"RNA\"<\/span>, beta =0.5<\/span>, <\/span><\/code><code> batchEstimation =FALSE<\/span>, filterNoise =TRUE<\/span>) <\/span><\/code><code>plot(arsyn_3, typeP=\"pca.cor\"<\/span>, bty =\"L\"<\/span>, <\/span><\/code><code> pch = custom_pch, cex =3<\/span>, col.per.group = custom_col, <\/span><\/code><code> legend.text =c(\"Color: Batch\"<\/span>, names(data_RNA$ListOfBatches), <\/span><\/code><code> \"Fill: Cond.\"<\/span>, unique(colData(data_RNA$ListOfBatches$A)$tfactor)), <\/span><\/code><code> args.legend =list<\/span>(\"x\"<\/span>=\"topright\"<\/span>, <\/span><\/code><code> \"pch\"<\/span>=c(NA, 15<\/span>, 15<\/span>, 15<\/span>, <\/span><\/code><code> NA, 15<\/span>, 0<\/span>), <\/span><\/code><code> \"col\"<\/span>=c(NA, \"brown2\"<\/span>, \"dodgerblue\"<\/span>, \"forestgreen\"<\/span>, <\/span><\/code><code> NA, 1<\/span>, 1<\/span>), <\/span><\/code><code> \"bty\"<\/span>=\"n\"<\/span>, <\/span><\/code><code> \"cex\"<\/span>=1.2<\/span>)) <\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014464\" data-ratio=\"0.5611111111111111\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_zgInvjRdiadJjBDzrk7KOeswjNVnhg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVScszXMnNJxkqbE0GtrCcfXz7umzgInvjRdiadJjBDzrk7KOeswjNVnhg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"314.3999938964844\" width=\"560.010009765625\" \/><\/span><span style=\"font-family: mp-quote, -apple-system-font, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Hiragino Sans GB", "Microsoft YaHei UI", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 0.034em;text-align: justify;font-size: 15px;\"> <\/span><\/span> <\/p>\n\u56fe4\uff1a<\/span>\u566a\u58f0\u51cf\u5c11\u6a21\u5f0f<\/span> <\/span><\/span><\/p>\n\u5de6\uff1a\u65b9\u5dee\u89e3\u91ca\u56fe\u3002\u5f53 showplot = TRUE \u65f6\uff0c\u9ed8\u8ba4\u7ed8\u5236\u8be5\u56fe\u3002\u5b83\u8868\u793a\u6b8b\u5dee\u4e2d\u53ef\u53d8\u6027\u7684\u767e\u5206\u6bd4\uff08y \u8f74\uff09\uff0c\u7531\u5177\u6709\u7ed9\u5b9a\u4e3b\u6210\u5206\u6570\u76ee\u7684\u6a21\u578b\u89e3\u91ca\uff08x \u8f74\uff09\u3002\u6700\u7ec8\u6a21\u578b\u4e2d\u9009\u62e9\u7684\u7ec4\u4ef6\u6570\u7528\u4e09\u89d2\u5f62\u7b26\u53f7\u8868\u793a\uff0c\u5e76\u8ba1\u7b97\u4e3a\u89e3\u91ca beta \u500d\u6b8b\u5dee\u5e73\u5747\u53ef\u53d8\u6027\u3002\u53f3\uff1a\u4fee\u6b63\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684 PCA \u56fe\u3002 \u5728\u30104\u3011\u56fe\u4e2d\uff0c\u6211\u4eec\u53ef\u4ee5\u770b\u5230\uff0c\u5c3d\u7ba1\u8fd9\u4e2a\u6279\u6b21\u88ab\u8ba4\u4e3a\u662f\u4e0d\u660e\u786e\u7684(batchEstimation=FALSE)\uff0c\u4f46\u662fARSyN\u5df2\u7ecf\u901a\u8fc7\u4f30\u8ba1\u4e0d\u9700\u8981\u53d8\u5316\u7684\u4e3b\u8981\u6765\u6e90\uff0c\u4ece\u6570\u636e\u4e2d\u6d88\u9664\u4e86\u566a\u58f0\u3002\u5728\u8fd9\u79cd\u566a\u58f0\u51cf\u5c11\u6a21\u5f0f\u4e0b\uff0c\u6211\u4eec\u53ef\u4ee5\u901a\u8fc7beta\u53c2\u6570\u6765\u8c03\u6574\u6b8b\u5dee\u4e2d\u5269\u4f59\u566a\u58f0\u7684\u5e45\u5ea6\u3002\u57fa\u672c\u4e0a\uff0c\u8d85\u8fc7beta\u500d\u7684\u5e73\u5747\u53d8\u5f02\u6027\u7684\u6210\u5206\u88ab\u786e\u5b9a\u4e3a\u6b8b\u5dee\u4e2d\u7684\u7cfb\u7edf\u566a\u58f0(\u5728\u8fd9\u4e2a\u6a21\u578b\u4e2d\u9009\u62e9\u4e863\u4e2a\u6210\u5206)\u3002\u56e0\u6b64\uff0cbeta\u503c\u8d8a\u5927\uff0c\u5bfc\u81f4\u6b8b\u5dee\u4e2d\u9009\u62e9\u66f4\u5c11\u7684\u6210\u5206\u3002<\/span><\/span><\/p>\nARSyNbac\u4e24\u79cd\u6a21\u5f0f<\/strong><\/span><\/p>\n\u5982\u679c\u6279\u6b21\u6548\u5e94\u7684\u6765\u6e90\u5df2\u77e5\uff0c\u4f46\u53ef\u80fd\u5b58\u5728\u4e00\u4e2a\u989d\u5916\u7684\u672a\u77e5\u7684\u4e0d\u9700\u8981\u7684\u53d8\u5f02\u6e90\uff0c<\/span>ARSyNbac<\/span>\u53ef\u4ee5\u901a\u8fc7\u8bbe\u7f6e<\/span>batchEstimation = TRUE<\/span>\u548c<\/span>filterNoise = TRUE<\/span>\u6765\u6267\u884c\u524d\u4e24\u79cd\u65b9\u6cd5\u3002\u8bf7\u6ce8\u610f\uff0c\u5982\u679c\u5df2\u77e5\u7684\u6279\u6b21\u6548\u5e94\u5e76\u4e0d\u4ee3\u8868\u6211\u4eec\u6570\u636e\u4e2d\u7684\u4e3b\u8981\u566a\u58f0\u6e90\uff0c\u8fd9\u79cd\u6a21\u5f0f\u4e5f\u53ef\u80fd\u662f\u6709\u7528\u7684\u3002<\/span><\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code>par(mfrow =c(1<\/span>,2<\/span>)) <\/span><\/code><code>arsyn_4 <-ARSyNbac(data_RNA, modelName =\"RNA\"<\/span>, beta =0.5<\/span>, <\/span><\/code><code> batchEstimation =TRUE<\/span>, filterNoise =TRUE<\/span>, <\/span><\/code><code> Interaction =TRUE<\/span>, <\/span><\/code><code> Variability =0.95<\/span>) <\/span><\/code><code>plot(arsyn_4, typeP=\"pca.cor\"<\/span>, bty =\"L\"<\/span>, <\/span><\/code><code> pch = custom_pch, cex =3<\/span>, col.per.group = custom_col, <\/span><\/code><code> legend.text =c(\"Color: Batch\"<\/span>, names(data_RNA$ListOfBatches), <\/span><\/code><code> \"Fill: Cond.\"<\/span>, unique(colData(data_RNA$ListOfBatches$A)$tfactor)), <\/span><\/code><code> args.legend =list<\/span>(\"x\"<\/span>=\"topright\"<\/span>, <\/span><\/code><code> \"pch\"<\/span>=c(NA, 15<\/span>, 15<\/span>, 15<\/span>, <\/span><\/code><code> NA, 15<\/span>, 0<\/span>), <\/span><\/code><code> \"col\"<\/span>=c(NA, \"brown2\"<\/span>, \"dodgerblue\"<\/span>, \"forestgreen\"<\/span>, <\/span><\/code><code> NA, 1<\/span>, 1<\/span>), <\/span><\/code><code> \"bty\"<\/span>=\"n\"<\/span>, <\/span><\/code><code> \"cex\"<\/span>=1.2<\/span>))<\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\"><\/span><o:page><\/o:page><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014470\" data-ratio=\"0.5611111111111111\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_ibNkicYVbDVCHvAzVOrytCPbhiaZXg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSHbYevicvvA7mbPAf8bw4XACfVpN4ibNkicYVbDVCHvAzVOrytCPbhiaZXg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"313.9999694824219\" width=\"560.010009765625\" \/><\/span> <\/span>\u56fe5\uff1a<\/span>\u4e24\u79cd\u6a21\u5f0f\u7ed3\u5408<\/span><\/span><\/p>\n<p style=\"margin-top: 9.0pt;margin-bottom: 9.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\">\u5de6\u56fe\uff1a\u65b9\u5dee\u89e3\u91ca\u56fe\u3002\u5f53 showplot = TRUE \u65f6\uff0c\u9ed8\u8ba4\u663e\u793a\u8be5\u56fe\u3002\u56fe\u4e2d\u8868\u793a\u7684\u662f\u67d0\u4e00\u6a21\u578b\u5bf9\u6b8b\u5dee\u53d8\u5f02\u7684\u89e3\u91ca\u767e\u5206\u6bd4\uff08y\u8f74\uff09\uff0c\u968f\u7740\u4e3b\u6210\u5206\u6570\u76ee\u7684\u589e\u52a0\uff08x\u8f74\uff09\u3002\u6700\u7ec8\u6a21\u578b\u6240\u9009\u5b9a\u7684\u4e3b\u6210\u5206\u6570\u76ee\u7528\u4e09\u89d2\u5f62\u7b26\u53f7\u8868\u793a\uff0c\u5e76\u8ba1\u7b97\u89e3\u91cabeta\u500d\u6b8b\u5dee\u53d8\u5f02\u7684\u5e73\u5747\u503c\u3002<\/span><\/p>\n<p style=\"margin-top: 9.0pt;margin-bottom: 9.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\">\u53f3\u56fe\uff1a\u4fee\u6b63\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684PCA\u56fe\u3002 \u5728\u56fe5\u4e2d\uff0c\u6211\u4eec\u53ef\u4ee5\u770b\u5230\uff0c\u540c\u65f6\u6267\u884c\u4e24\u79cd\u65b9\u6cd5\u65f6\uff0cARSyNbac\u8fbe\u5230\u4e86PC1\u65b9\u5dee\u7684\u6700\u5927\u89e3\u91ca\u7387\uff08\u7279\u522b\u662f\u4e0e\u56fe3\u76f8\u6bd4\uff09\u3002\u5728\u8fd9\u79cd\u6a21\u5f0f\u4e0b\uff0c\u6211\u4eec\u53ef\u4ee5\u5229\u7528\u03b2\u53c2\u6570\u548c\u4e0e\u89e3\u91ca\u65b9\u5dee\u76f8\u5173\u7684\u6279\u6b21\u6548\u5e94\u6765\u8c03\u6574\u6b8b\u5dee\u566a\u58f0\u53bb\u9664\u7684\u7a0b\u5ea6\u3002\u5728\u8fd9\u4e2a\u4f8b\u5b50\u4e2d\uff0c\u5982\u56fe4\u6240\u793a\uff0c\u5df2\u77e5\u6279\u6b21\u6548\u5e94\u662f\u4e3b\u8981\uff08\u51e0\u4e4e\u662f\u552f\u4e00\u7684\uff09\u4e0d\u9700\u8981\u7684\u53d8\u5f02\u6e90\u3002\u56e0\u6b64\uff0c\u5728\u5176\u4ed6\u5177\u6709\u591a\u4e2a\u6279\u6b21\u6e90\u7684\u60c5\u51b5\u4e0b\uff0c\u8fd9\u79cd\u6a21\u5f0f\u7684\u7ed3\u679c\u53ef\u80fd\u4e0e\u4e4b\u524d\u7684\u4e24\u79cd\u64cd\u4f5c\u65b9\u5f0f\u975e\u5e38\u4e0d\u540c\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n\u591a\u7ec4\u5b66\u6570\u636e\u96c6\u4e0a\u7684\u6279\u6b21\u6548\u5e94\u6821\u6b63<\/strong><\/span><\/p>\n\u5173\u4e8eMultiBaC<\/strong><\/span><\/p>\nMultiBaC \u65b9\u6cd5\u6982\u8ff0<\/span><\/p>\nMultiBaC\u662f\u4e00\u79cd\u4ece\u591a\u7ec4\u5b66\u6570\u636e\u4e2d\u63a8\u65ad\u7ec6\u83cc\u7fa4\u843d\u8c03\u63a7\u903b\u8f91\u7684\u8ba1\u7b97\u65b9\u6cd5\u3002 \u591a\u7ec4\u5b66\u6570\u636e\u6574\u5408\u5df2\u6210\u4e3a\u7406\u89e3\u751f\u7269\u7cfb\u7edf\u5de5\u4f5c\u673a\u5236\u7684\u6d41\u884c\u65b9\u6cd5\u3002\u7136\u800c\uff0c\u751f\u6210\u8fd9\u7c7b\u6570\u636e\u96c6\u4ecd\u7136\u6210\u672c\u9ad8\u4e14\u8017\u65f6\u3002\u56e0\u6b64\uff0c\u975e\u5e38\u5e38\u89c1\u7684\u60c5\u51b5\u662f\uff0c\u5e76\u975e\u6240\u6709\u6837\u672c\u6216\u7ec4\u5b66\u6570\u636e\u7c7b\u578b\u540c\u65f6\u4ea7\u751f\u6216\u5728\u540c\u4e00\u5b9e\u9a8c\u5ba4\u4ea7\u751f\uff0c\u800c\u662f\u5206\u6279\u8fdb\u884c\u3002\u6b64\u5916\uff0c\u5f53\u7814\u7a76\u56e2\u961f\u65e0\u6cd5\u751f\u6210\u81ea\u5df1\u7684\u591a\u7ec4\u5b66\u6570\u636e\u96c6\u65f6\uff0c\u4ed6\u4eec\u901a\u5e38\u4ece\u4e0d\u540c\u7684\u516c\u5171\u5b58\u50a8\u5e93\u6536\u96c6\uff0c\u56e0\u6b64\u6765\u81ea\u4e0d\u540c\u7684\u7814\u7a76\u6216\u5b9e\u9a8c\u5ba4\uff08\u4e5f\u662f\u6765\u81ea\u4e0d\u540c\u7684\u6279\u6b21\uff09\u3002\u5728\u8fd9\u4e24\u79cd\u60c5\u51b5\u4e0b\uff0c\u90fd\u9700\u8981\u4e8b\u5148\u4ece\u8fd9\u4e9b\u6570\u636e\u96c6\u4e2d\u53bb\u9664\u6279\u6b21\u6548\u5e94\u4ee5\u6210\u529f\u8fdb\u884c\u6570\u636e\u6574\u5408\u3002\u7ea0\u6b63\u5355\u4e00\u6570\u636e\u7c7b\u578b\u7684\u6279\u6b21\u6548\u5e94\u7684\u65b9\u6cd5\u65e0\u6cd5\u5e94\u7528\u4e8e\u7ea0\u6b63\u8de8\u7ec4\u5b66\u7684\u6279\u6b21\u6548\u5e94\uff0c\u56e0\u6b64\u6211\u4eec\u5f00\u53d1\u4e86MultiBaC\u7b56\u7565\uff0c\u8be5\u7b56\u7565\u53ef\u7ea0\u6b63\u5206\u5e03\u5728\u4e0d\u540c\u5b9e\u9a8c\u5ba4\u6216\u6570\u636e\u91c7\u96c6\u4e8b\u4ef6\u4e2d\u7684\u591a\u7ec4\u5b66\u6570\u636e\u96c6\u4e2d\u7684\u6279\u6b21\u6548\u5e94\u3002 \u7136\u800c\uff0c\u5bf9\u4e8e\u591a\u7ec4\u5b66\u6570\u636e\u96c6\u6709\u4e00\u4e9b\u8981\u6c42\uff0c\u4ee5\u4fbf\u4f7f\u7528MultiBaC\u53bb\u9664\u8de8\u7ec4\u5b66\u7684\u6279\u6b21\u6548\u5e94\uff1a<\/span><\/p>\n\u2022\u6bcf\u4e2a\u6279\u6b21\u4e2d\u5fc5\u987b\u81f3\u5c11\u6709\u4e00\u79cd\u5e38\u89c1\u7ec4\u5b66\u6570\u636e\u7c7b\u578b\u3002\u4f8b\u5982\uff0c\u6211\u4eec\u53ef\u80fd\u5728\u6240\u6709\u6279\u6b21\u4e2d\u90fd\u6709\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u6d4b\u91cf\uff0c\u7136\u540e\u5728\u6bcf\u4e2a\u6279\u6b21\u4e2d\u5177\u6709\u5176\u4ed6\u4e0d\u540c\u7684\u7ec4\u5b66\u6570\u636e\u7c7b\u578b\u3002\u4e0d\u5fc5\u8981\u6c42\u4f7f\u7528\u76f8\u540c\u7684\u6280\u672f\u6765\u6d4b\u91cf\u5171\u540c\u7684\u7ec4\u5b66\uff08\u4f8b\u5982\u57fa\u56e0\u8868\u8fbe\uff09\u3002\u4f8b\u5982\uff0c\u6211\u4eec\u53ef\u4ee5\u6709\u4e00\u4e2a\u6279\u6b21\u4e2d\u7684\u5fae\u9635\u5217\u8868\u8fbe\u6570\u636e\u548c\u53e6\u4e00\u4e2a\u6279\u6b21\u4e2d\u7684RNA-seq\u6570\u636e\u3002<\/span><\/p>\n\u2022\u5bf9\u4e8e\u6240\u6709\u5e38\u89c1\u6570\u636e\u77e9\u9635\uff0c\u7ec4\u5b66\u7279\u5f81\u6807\u8bc6\u7b26\u5fc5\u987b\u76f8\u540c\u3002\u4f8b\u5982\uff0c\u6211\u4eec\u4e0d\u80fd\u5728\u4e00\u4e2a\u6279\u6b21\u4e2d\u4f7f\u7528Ensembl\u6807\u8bc6\u7b26\uff0c\u800c\u5728\u53e6\u4e00\u4e2a\u6279\u6b21\u4e2d\u4f7f\u7528RefSeq\u3002\u4e0d\u5fc5\u8981\u6c42\u6240\u6709\u6279\u6b21\u4e2d\u5177\u6709\u76f8\u540c\u6570\u91cf\u7684\u7ec4\u5b66\u7279\u5f81\uff0c\u4f8b\u5982\u57fa\u56e0\u3002MultiBac\u5c06\u4ece\u6240\u6709\u5e38\u89c1\u6570\u636e\u7c7b\u578b\u77e9\u9635\u4e2d\u63d0\u53d6\u516c\u5171\u6807\u8bc6\u7b26\u4ee5\u6267\u884c\u5206\u6790\u3002<\/span><\/p>\n\u2022\u5728\u540c\u4e00\u6279\u6b21\u4e2d\uff0c\u5b9e\u9a8c\u8bbe\u8ba1\u5bf9\u4e8e\u8be5\u6279\u6b21\u4e2d\u7684\u6240\u6709\u7ec4\u5b66\u90fd\u5fc5\u987b\u76f8\u540c\uff0c\u5373\u76f8\u540c\u7684\u5b9e\u9a8c\u7ec4\uff0c\u5177\u6709\u76f8\u540c\u6570\u91cf\u7684\u6765\u81ea\u76f8\u540c\u4e2a\u4f53\u7684\u91cd\u590d\u3002\u6240\u6709\u8fd9\u4e9b\u6837\u672c\u5728\u6240\u6709\u7ec4\u5b66\u6570\u636e\u77e9\u9635\u4e2d\u90fd\u5fc5\u987b\u4ee5\u76f8\u540c\u7684\u987a\u5e8f\u6392\u5217\u3002<\/span><\/p>\n\u793a\u4f8b\uff1a\u9175\u6bcd\u591a\u7ec4\u5b66\u6570\u636e\u96c6<\/strong><\/span><\/p>\n\u8fd9\u4e9b\u6570\u636e\u5305\u62ec\u57fa\u56e0\u8868\u8fbe\u6570\u636e\uff08RNA\uff09\uff0c\u4ee5\u53ca\u7531\u4e0d\u540c\u5b9e\u9a8c\u5ba4\u5206\u522b\u4ea7\u751f\u7684\u4e0d\u540c\u5176\u4ed6\u7ec4\u5b66\u6570\u636e\u7c7b\u578b\u3002\u5b9e\u9a8c\u5ba4A\u6536\u96c6\u4e86\u8f6c\u5f55\u901f\u7387\u6570\u636e\uff08GRO\uff0c\u5b58\u53d6\u53f7GSE1002\uff09[<\/span>2<\/span>]\u3002\u5b9e\u9a8c\u5ba4B\u83b7\u5f97\u4e86\u7ffb\u8bd1\u901f\u7387\u6570\u636e\uff08RIBO\uff0c\u5b58\u53d6\u53f7GSE56622\uff09[<\/span>5<\/span>]\u3002\u6700\u540e\uff0c\u5b9e\u9a8c\u5ba4C\u6d4b\u91cf\u4e86\u5168\u5c40PAR-CLIP\u6570\u636e\uff08PAR-CLIP\uff0c\u5b58\u53d6\u53f7GSE43747\uff09[<\/span>6<\/span>]\u3002\u56e0\u6b64\uff0c\u8fd9\u4e9b\u5b9e\u9a8c\u5ba4\u5171\u4eab\u4e00\u4e2a\u6570\u636e\u7c7b\u578b\uff08RNA\uff09\uff0c\u800c\u5176\u4ed6\u6570\u636e\u7c7b\u578b\u5219\u5404\u4e0d\u76f8\u540c\uff08GRO\u3001RIBO\u548cPAR-CLIP\uff09\u3002\u8fd9\u79cd\u5206\u5e03\u5f0f\u591a\u7ec4\u5b66\u65b9\u6848\u4ee3\u8868\u4e86MultiBaC\u6240\u89e3\u51b3\u7684\u6821\u6b63\u95ee\u9898\u3002\u6570\u636e\u7ed3\u6784\u7684\u793a\u610f\u56fe\u53ef\u89c1\u4e8e\u56fe <\/span>6<\/span>\u3002 <img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014469\" data-ratio=\"0.4675925925925926\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_PFOIdFy6bZ8PUeLf9IHVFxFLib8NWg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSMCfw48LfobHuUPKMXHxRPLRTIPFOIdFy6bZ8PUeLf9IHVFxFLib8NWg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"262.0\" width=\"560.010009765625\" \/> <\/span>\u56fe6\uff1a<\/span>\u9175\u6bcd\u4f8b\u6570\u636e\u7ed3\u6784\u7684\u65b9\u6848<\/span><\/span><\/p>\n\u6b64\u9175\u6bcd\u591a\u7ec4\u5b66\u6570\u636e\u5305\u542b\u5728<\/span><span style=\"font-size: 15px;letter-spacing: 0.034em;font-family: Cambria;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;font-weight: bold;\">MutiBaC<\/span>\u5305\u4e2d\uff0c\u7528\u6765\u8bf4\u660e\u6b64\u5305\u7684\u4f7f\u7528\u65b9\u6cd5\u3002\u8fd9\u516d\u4e2a\u77e9\u9635\u53ef\u4ee5\u901a\u8fc7\u4f7f\u7528 <\/span><span style=\"font-size: 15px;letter-spacing: 0.034em;font-family: Cambria;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;font-style: italic;\">data(\u201cmultiyeast\u201d)<\/span>\u6307\u4ee4\u6765\u52a0\u8f7d\u3002<\/span><\/p>\nMultiBaC\u8f93\u5165\u6570\u636e<\/strong><\/span><\/p>\n\u5982\u524d\u6240\u8ff0\uff0c<\/span>MultiBaC<\/span>\u5305\u4f7f\u7528<\/span>MultiAssayExperiment<\/span>\u5bf9\u8c61\uff0c\u8fd9\u662fBioconductor\u4e2d\u7528\u4e8e\u591a\u7ec4\u5b66\u7814\u7a76\u7684\u4e00\u79cd\u5bb9\u5668\u7c7b\u578b\uff0c\u53ef\u4ee5\u4ece\u4e00\u4e2a\u7531\u77e9\u9635\u6216<\/span>data.frame<\/span>\u5bf9\u8c61\u7ec4\u6210\u7684\u5217\u8868\u4e2d\u521b\u5efa\u3002\u8fd9\u4e9b\u77e9\u9635\u5fc5\u987b\u5177\u6709\u4ee5\u884c\u4e3a\u7279\u5f81\u3001\u4ee5\u5217\u4e3a\u6837\u672c\u7684\u7279\u70b9\uff08\u8bf7\u53c2\u89c1ARSyNbac\u90e8\u5206\u4e2d\u7684\u793a\u4f8b\uff09\u3002\u7531\u4e8e<\/span>MultiBaC<\/span>\u5728\u76f8\u540c\u6279\u6b21\u7684\u4e0d\u540c\u7ec4\u5b66\u4e4b\u95f4\u8ba1\u7b97\u56de\u5f52\u6a21\u578b\uff0c\u56e0\u6b64\u91cd\u8981\u7684\u662f\u6765\u81ea\u76f8\u540c\u6279\u6b21\u7684\u6240\u6709\u77e9\u9635\u5fc5\u987b\u5177\u6709\u76f8\u540c\u7684\u5b9e\u9a8c\u8bbe\u8ba1\uff1a\u76f8\u540c\u6570\u91cf\u7684\u6837\u672c\u5e76\u4ee5\u76f8\u540c\u7684\u987a\u5e8f\u6392\u5217\u3002<\/span>MultiBaC<\/span>\u4e5f\u6d89\u53ca\u4e0d\u540c\u6279\u6b21\u7684\u4e0d\u540c\u7ec4\u5b66\u7684\u5171\u4fe1\u606f\u3002\u56e0\u6b64\uff0c\u5982\u679c\u7ec4\u5b66\u53d8\u91cf\u7684\u6570\u91cf\u548c\u987a\u5e8f\u4e0d\u540c\uff0c\u5219<\/span>MultiBaC<\/span>\u5c06\u9009\u62e9\u5171\u6709\u7684\u53d8\u91cf\u7528\u4e8e\u6a21\u578b\u3002\u56e0\u6b64\uff0c\u5fc5\u987b\u4f7f\u7528\u76f8\u540c\u7c7b\u578b\u7684\u6807\u8bc6\u7b26\u5bf9\u884c\u8fdb\u884c\u547d\u540d\u3002 \u8981\u751f\u6210\u4f5c\u4e3aMultiBaC\u51fd\u6570\u8f93\u5165\u7684<\/span>mbac<\/span>\u5bf9\u8c61\uff0c\u53ef\u4ee5\u4f7f\u7528\u5305\u4e2d\u7684<\/span>createMbac<\/span>\u51fd\u6570\uff0c\u8f7b\u677e\u4fbf\u6377\u5730\u5b8c\u6210\u8fd9\u9879\u4efb\u52a1\u3002<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"swift\"><code>my_mbac <- createMbac (inputOmics = list(A<\/span>.rna, A<\/span>.gro, <\/span><\/code><code> B<\/span>.rna, B<\/span>.ribo, <\/span><\/code><code> C<\/span>.rna, C<\/span>.par), <\/span><\/code><code> batchFactor = c<\/span>(\"A\"<\/span>, \"A\"<\/span>, <\/span><\/code><code> \"B\"<\/span>, \"B\"<\/span>, <\/span><\/code><code> \"C\"<\/span>, \"C\"<\/span>), <\/span><\/code><code> experimentalDesign = list(\"A\"<\/span> = c<\/span>(\"Glu+\"<\/span>, \"Glu+\"<\/span>, <\/span><\/code><code> \"Glu+\"<\/span>, \"Glu-\"<\/span>, <\/span><\/code><code> \"Glu-\"<\/span>, \"Glu-\"<\/span>), <\/span><\/code><code> \"B\"<\/span> = c<\/span>(\"Glu+\"<\/span>, \"Glu+\"<\/span>, <\/span><\/code><code> \"Glu-\"<\/span>, \"Glu-\"<\/span>), <\/span><\/code><code> \"C\"<\/span> = c<\/span>(\"Glu+\"<\/span>, \"Glu+\"<\/span>, <\/span><\/code><code> \"Glu-\"<\/span>, \"Glu-\"<\/span>)), <\/span><\/code><code> omicNames = c<\/span>(\"RNA\"<\/span>, \"GRO\"<\/span>, <\/span><\/code><code> \"RNA\"<\/span>, \"RIBO\"<\/span>, <\/span><\/code><code> \"RNA\"<\/span>, \"PAR\"<\/span>)) <\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\"><\/span><o:page><\/o:page><\/p>\n\u6709\u5173\u201ccreateMbac\u201d\u51fd\u6570\u7684\u66f4\u591a\u8be6\u7ec6\u4fe1\u606f\uff0c\u8bf7\u53c2\u89c1ARSyNbac\u8f93\u5165\u6570\u636e\u90e8\u5206\u3002\u9700\u8981\u6ce8\u610f\u7684\u662f\uff0c\u6211\u4eec\u4e0d\u9700\u8981\u6307\u660e\u54ea\u4e2a\u662f\u5e38\u89c1\u7684omic\uff08\u5728commonOmic\u53c2\u6570\u4e2d\uff09\uff0c\u56e0\u4e3a\u5bf9\u4e8e\u6240\u6709\u6279\u6b21\uff08\u5b9e\u9a8c\u5ba4\uff09\u6765\u8bf4\uff0c\u53ea\u6709\u4e00\u4e2a\u5171\u540c\u7684omic\uff08RNA\uff09\uff0c\u5e76\u4e14\u8be5\u51fd\u6570\u5c06\u5176\u68c0\u6d4b\u4e3a\u5e38\u89c1\u7684omic\u3002<\/span><\/p>\nMultiBaC correction<\/strong><\/span><\/p>\n\u4e00\u65e6\u4f7f\u7528\u201ccreateMbac\u201d\u51fd\u6570\u521b\u5efa\u4e86<\/span>mbac<\/span>\u5bf9\u8c61\uff0c\u5c31\u53ef\u4ee5\u5c06\u5176\u7528\u4f5c\u201cMultiBaC\u201d\u51fd\u6570\u7684\u8f93\u5165\u6570\u636e\uff08\u4ee5<\/span>mbac<\/span>\u53c2\u6570\u7684\u5f62\u5f0f\uff09\uff0c\u800c\u201cMultiBaC\u201d\u51fd\u6570\u662f\u7528\u4e8e\u6821\u6b63\u591a\u7ec4\u5b66\u6279\u6b21\u6548\u5e94\u7684\u5305\u88c5\u51fd\u6570\u3002<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code>MultiBaC (mbac, <\/span><\/code><code> test.comp = NULL<\/span>, scale = FALSE<\/span>, <\/span><\/code><code> center = TRUE<\/span>, crossval = NULL<\/span>, <\/span><\/code><code> Interaction = FALSE<\/span>, <\/span><\/code><code> Variability = 0.90<\/span>, <\/span><\/code><code> showplot = TRUE<\/span>, <\/span><\/code><code> showinfo = TRUE<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\"><span style=\"font-size: 15px;letter-spacing: 0.034em;text-align: justify;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;font-style: italic;\">MultiBaC<\/span>\u51fd\u6570\u7684\u53c2\u6570\u5bf9\u5e94\u4e8eMultiBaC\u65b9\u6cd5\u7684\u5404\u4e2a\u6b65\u9aa4\uff1a<\/span><\/span><\/p>\n\u2022<\/span>mbac<\/span>: \u7531 <\/span>createMbac<\/span> \u751f\u6210\u7684 mbac \u5bf9\u8c61\u3002<\/span><\/span><\/p>\n\u2022<\/span>test.comp<\/span>: PLS \u6a21\u578b\u5141\u8bb8\u7684\u6700\u5927\u7ec4\u4ef6\u6570\u3002\u5982\u679c\u4e3a NULL\uff08\u9ed8\u8ba4\uff09\uff0c\u5219\u4f7f\u7528\u77e9\u9635\u7684\u6700\u5c0f\u6709\u6548\u79e9\u4f5c\u4e3a\u6700\u5927\u7ec4\u4ef6\u6570\u3002<\/span><\/span><\/p>\n\u2022<\/span>scale<\/span>: \u903b\u8f91\u503c\u3002\u662f\u5426\u9700\u8981\u5bf9 X \u548c Y \u77e9\u9635\u8fdb\u884c\u7f29\u653e\u3002\u9ed8\u8ba4\u503c\u4e3a FALSE\u3002<\/span><\/span><\/p>\n\u2022<\/span>center<\/span>: \u903b\u8f91\u503c\u3002\u662f\u5426\u9700\u8981\u5bf9 X \u548c Y \u77e9\u9635\u8fdb\u884c\u4e2d\u5fc3\u5316\u3002\u9ed8\u8ba4\u503c\u4e3a TRUE\u3002<\/span><\/span><\/p>\n\u2022<\/span>crossval<\/span>: \u6574\u6570\uff1a\u4ea4\u53c9\u9a8c\u8bc1\u6bb5\u6570\u3002\u6837\u672c\u6570\uff08\u201cx\u201d\u7684\u884c\u6570\uff09\u5fc5\u987b >= crossvalI\u3002\u5982\u679c\u4e3a NULL\uff08\u9ed8\u8ba4\uff09\uff0c\u5219\u6267\u884c leave-one-out \u4ea4\u53c9\u9a8c\u8bc1\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n\u2022<\/span>Interaction<\/span>: \u903b\u8f91\u503c\u3002\u662f\u5426\u5728 ARSyN \u6a21\u578b\u4e2d\u5efa\u7acb\u5b9e\u9a8c\u56e0\u7d20\u548c\u6279\u6b21\u56e0\u7d20\u4e4b\u95f4\u7684\u76f8\u4e92\u4f5c\u7528\u6a21\u578b\u3002\u9ed8\u8ba4\u503c\u4e3a FALSE\u3002<\/span><\/span><\/p>\n\u2022<\/span>Variability<\/span>: \u4ece 0 \u5230 1 \u7684\u6700\u5c0f\u767e\u5206\u6bd4\u6570\u636e\u53d8\u5316\u6027\uff0c\u5bf9\u4e8e\u6bcf\u4e2a ARSyN \u6a21\u578b\u5fc5\u987b\u89e3\u91ca\u3002\u9ed8\u8ba4\u503c\u4e3a 0.90\u3002<\/span><\/span><\/p>\n\u2022<\/span>showplot<\/span>: \u903b\u8f91\u503c\u3002\u5982\u679c\u4e3a TRUE\uff08\u9ed8\u8ba4\uff09\uff0c\u5219\u663e\u793a Q2 \u548c\u89e3\u91ca\u65b9\u5dee\u56fe\u3002<\/span><\/span><\/p>\n\u2022<\/span>showinfo<\/span>: \u903b\u8f91\u503c\u3002\u5982\u679c\u4e3a TRUE\uff08\u9ed8\u8ba4\uff09\uff0c\u5219\u663e\u793a\u51fd\u6570\u8fdb\u5ea6\u4fe1\u606f\u3002 \u4e0b\u9762\u663e\u793a\u4e86\u4f7f\u7528MultiBaC\u51fd\u6570\u5bf9\u9175\u6bcd\u793a\u4f8b\u6570\u636e\u8fdb\u884c\u5904\u7406\u7684\u60c5\u51b5\uff1a<\/span><\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code>my_final_mbac <-MultiBaC (my_mbac, <\/span><\/code><code> test.comp =NULL, scale =FALSE, <\/span><\/code><code> center =TRUE, crossval =NULL, <\/span><\/code><code> Interaction =TRUE, <\/span><\/code><code> Variability =0.9, <\/span><\/code><code> showplot =TRUE, <\/span><\/code><code> showinfo =TRUE) <\/span><\/code><code>#<\/span># Step 1: Create PLS models <\/span><\/span><\/code><code>#<\/span># - Model for batch A <\/span><\/span><\/code><code>#<\/span># - Model for batch B <\/span><\/span><\/code><code>#<\/span># - Model for batch C <\/span><\/span><\/code><code>#<\/span># Step 2: Generating missing omics <\/span><\/span><\/code><code>#<\/span># Step 3: Batch effect correction using ARSyNbac <\/span><\/span><\/code><code>#<\/span># [1] \"Table: Inner correlation between scores for each PLS model computed.\" <\/span><\/span><\/code><code>#<\/span># <\/span><\/span><\/code><code>#<\/span># <\/span><\/span><\/code><code>#<\/span># A: GRO B: RIBO C: PAR <\/span><\/span><\/code><code>#<\/span># ------------- ---------- ---------- ---------- <\/span><\/span><\/code><code>#<\/span># Component: 1 0.9471967 0.9987790 0.9396986 <\/span><\/span><\/code><code>#<\/span># Component: 2 0.9277123 0.9991239 0.9998556 <\/span><\/span><\/code><code>#<\/span># Component: 3 0.9992129 1.0000000 1.0000000 <\/span><\/span><\/code><code>#<\/span># Component: 4 0.9999867 NA NA <\/span><\/span><\/code><code>#<\/span># Component: 5 1.0000000 NA NA <\/span><\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014471\" data-ratio=\"0.5611111111111111\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/10_um1skko71F9zbUNmLTgWxYTLhK3gqQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSxDhFxDldjkUocY1Dcf8GK0ayum1skko71F9zbUNmLTgWxYTLhK3gqQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"314.0\" width=\"560.010009765625\" \/><\/span> <\/span>\u56fe7\uff1a<\/span>Q2\u548c\u65b9\u5dee\u89e3\u91ca\u56fe<\/span><\/span><\/p>\n<p style=\"margin-top: 9.0pt;margin-bottom: 9.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\">Q2\u56fe\uff08\u5de6\uff09\u663e\u793a\u4e86\u8fbe\u5230\u4e00\u5b9aQ2\u503c\u6240\u9700\u7684\u7ec4\u4ef6\u6570\u91cf\uff08x\uff09\uff08y\uff09\u3002\u6bcf\u4e2a\u6a21\u578b\u6240\u9009\u7684\u7ec4\u4ef6\u6570\u91cf\u7528\u4e09\u89d2\u5f62\u7b26\u53f7\u8868\u793a\u3002\u7070\u8272\u7684\u865a\u7ebf\u8868\u793a0.7\u7684Q2\u9608\u503c\u3002\u65b9\u5dee\u89e3\u91ca\u56fe\uff08\u53f3\uff09\u8868\u793a\u4e86\u8981\u89e3\u91ca\u611f\u5174\u8da3\u7684\u6548\u5e94\uff08\u6279\u6b21\u6548\u5e94\uff09\u7684\u67d0\u4e2a\u53d8\u5f02\u6027\uff08y\uff09\u6240\u9700\u7684\u7ec4\u4ef6\u6570\u91cf\uff08x\uff09\u3002\u6bcf\u4e2a\u6a21\u578b\u6240\u9009\u7684\u7ec4\u4ef6\u6570\u91cf\u7528\u4e09\u89d2\u5f62\u7b26\u53f7\u8868\u793a\u3002\u7070\u8272\u7684\u865a\u7ebf\u8868\u793a\u65b9\u5dee\u53c2\u6570\u7684\u767e\u5206\u6bd4\u3002 \u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff08<\/span>showinfo = TRUE<\/span>\uff09\uff0c\u4f1a\u663e\u793a\u5305\u542bPLS\u6a21\u578b\u5185\u90e8\u76f8\u5173\u6027\u7684\u8868\u683c\u3002\u6b64\u5916\uff0c\u9ed8\u8ba4\u7684\u56fe\u5f62\uff08<\/span>showplot = TRUE<\/span>\uff09\u662f\u201cQ2\u56fe\u201d\u548c\u201c\u65b9\u5dee\u89e3\u91ca\u56fe\u201d\uff08\u53c2\u89c1\u56fe7\uff09\uff0c\u5176\u4e2d\u5305\u542b\u6709\u5173<\/span>MultiBaC<\/span>\u6027\u80fd\u7684\u91cd\u8981\u4fe1\u606f\u3002\u201cQ2\u56fe\u201d\u8868\u793aPLS\u6a21\u578b\u9884\u6d4b\u80fd\u529b\u7684Q2\u00b2\u5206\u6570\u3002x\u8f74\u8868\u793a\u63d0\u53d6\u7684PLS\u6a21\u578b\u7684\u7ec4\u4ef6\u6570\uff0cy\u8f74\u4e3aQ2\u00b2\u503c\u3002MultiBaC\u65b9\u6cd5\u7684\u6027\u80fd\u5c06\u968f\u7740Q2\u00b2\u503c\u7684\u589e\u52a0\u800c\u63d0\u9ad8\uff0c\u56e0\u4e3aQ2\u00b2\u503c\u9ad8\u8868\u660ePLS\u5bf9\u7f3a\u5931omics\u7684\u9884\u6d4b\u826f\u597d\uff0c\u56e0\u6b64\u53ef\u4ee5\u66f4\u597d\u5730\u4f30\u8ba1\u6279\u6b21\u6548\u5e94\u3002\u8bf7\u6ce8\u610f\uff0c\u6839\u636e\u77e9\u9635\u7684\u79e9\uff0c\u6bcf\u4e2aPLS\u6a21\u578b\u53ef\u80fd\u5177\u6709\u4e0d\u540c\u7684\u6700\u5927\u7ec4\u4ef6\u6570\u3002\u201c\u65b9\u5dee\u89e3\u91ca\u56fe\u201d\u63d0\u4f9b\u4e86\u4f7f\u7528ARSyN\u65b9\u6cd5\u63d0\u4f9b\u7684ASCA\u5206\u89e3\u89e3\u91ca\u7684\u4e0e\u6279\u6b21\u6548\u5e94\u76f8\u5173\u7684\u53d8\u5f02\u6027\u3002x\u8f74\u8868\u793a\u63d0\u53d6\u7684ASCA\u6a21\u578b\u7684\u7ec4\u4ef6\u6570\uff0cy\u8f74\u53cd\u6620\u4e86\u89e3\u91ca\u65b9\u5dee\u7684\u767e\u5206\u6bd4\u3002\u5728\u8fd9\u79cd\u60c5\u51b5\u4e0b\uff0c\u8f83\u9ad8\u7684\u89e3\u91ca\u65b9\u5dee\u5bfc\u81f4\u66f4\u597d\u7684\u6279\u6b21\u6548\u5e94\u4f30\u8ba1\u3002\u5728\u8fd9\u4e24\u4e2a\u56fe\u4e2d\uff0c\u6bcf\u4e2a\u6a21\u578b\u6240\u9009\u7684\u7ec4\u4ef6\u6570\u7528\u4e09\u89d2\u5f62\u7b26\u53f7\u8868\u793a\u3002\u5728\u201cQ2\u56fe\u201d\u4e2d\uff0c\u6240\u9009\u7684\u7ec4\u4ef6\u6570\u662f\u6700\u5927\u5316Q2\u503c\u7684\u7ec4\u4ef6\u6570\uff0c\u800c\u5728\u201c\u65b9\u5dee\u89e3\u91ca\u56fe\u201d\u4e2d\uff0c\u8fd9\u4e2a\u6570\u5b57\u662f\u6700\u5c0f\u6570\u91cf\u8fbe\u5230\u9ad8\u4e8e\u51fd\u6570<\/span>Variability<\/span>\u53c2\u6570\u7684\u89e3\u91ca\u65b9\u5dee\uff08\u7070\u8272\u7684\u865a\u7ebf\uff09\u7684\u7ec4\u4ef6\u6570\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n\u9010\u6b65\u8fd0\u884cMultiBaC\u6b65\u9aa4<\/strong><\/span><\/p>\nMultiBaC<\/span>\u7684\u6240\u6709\u4e0d\u540c\u6b65\u9aa4\u90fd\u53ef\u4ee5\u4f7f\u7528\u7279\u5b9a\u51fd\u6570\u4ece\u521d\u59cb\u7684<\/span>mbac<\/span>\u5bf9\u8c61\u72ec\u7acb\u8ba1\u7b97\u3002MultiBaC\u7b56\u7565\u53ef\u4ee5\u5206\u4e3a\u4e09\u4e2a\u4e3b\u8981\u6b65\u9aa4\uff0c\u4e0b\u9762\u5c06\u8be6\u7ec6\u63cf\u8ff0\uff1a1) PLS\u6a21\u578b\u62df\u5408\uff0c2) \u7f3a\u5931omics\u7684\u9884\u6d4b\uff0c3)\u6279\u6b21\u6548\u5e94\u4fee\u6b63\u3002 \u4ee5\u4e0b\u662f\u60a8\u8981\u6c42\u7684\u6bb5\u843d\u7684\u7ffb\u8bd1\uff1a<\/span><\/span><\/p>\nPLS\u6a21\u578b\u62df\u5408<\/span><\/p>\ngenModelList\u51fd\u6570\u5728\u4e0d\u540c\u548c\u5e38\u89c1\u7684omic\u6570\u636e\u7c7b\u578b\u4e4b\u95f4\u751f\u6210PLS\u6a21\u578b\uff0c\u5e76\u901a\u8fc7\u4ea4\u53c9\u9a8c\u8bc1\u65b9\u6cd5\u8ba1\u7b97\u6700\u4f73\u7ec4\u4ef6\u6570\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code>my_mbac_2 <- genModelList (my_mbac, test.comp = NULL<\/span>, <\/span><\/code><code> scale = FALSE<\/span>, center = TRUE<\/span>, <\/span><\/code><code> crossval = NULL<\/span>, <\/span><\/code><code> showinfo = TRUE<\/span>) <\/span><\/code><code>## - Model for batch A <\/span><\/span><\/code><code>## - Model for batch B <\/span><\/span><\/code><code>## - Model for batch C<\/span><\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\"><span style=\"font-size: 15px;letter-spacing: 0.034em;text-align: justify;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;font-style: italic;\">genModelList<\/span>\u51fd\u6570\u7684\u53c2\u6570\u4e3a\uff1a<\/span><\/p>\n\u2022<\/span>mbac<\/span>: \u5c5e\u4e8embac\u7c7b\u578b\u5bf9\u8c61\u3002<\/span><\/span><\/p>\n\u2022<\/span>test.comp<\/span>: PLS\u6a21\u578b\u4e2d\u5141\u8bb8\u7684\u6700\u5927\u7ec4\u4ef6\u6570\u3002\u5982\u679c\u4e3aNULL\uff08\u9ed8\u8ba4\u503c\uff09\uff0c\u5219\u4f7f\u7528\u77e9\u9635\u7684\u6700\u5c0f\u6709\u6548\u79e9\u4f5c\u4e3a\u6700\u5927\u7ec4\u4ef6\u6570\u3002<\/span><\/span><\/p>\n\u2022<\/span>scale<\/span>: \u903b\u8f91\u503c\u3002\u662f\u5426\u9700\u8981\u5bf9X\u548cY\u77e9\u9635\u8fdb\u884c\u7f29\u653e\u3002\u9ed8\u8ba4\u503c\u4e3aFALSE\u3002<\/span><\/span><\/p>\n\u2022<\/span>center<\/span>: \u903b\u8f91\u503c\u3002\u662f\u5426\u9700\u8981\u5bf9X\u548cY\u77e9\u9635\u8fdb\u884c\u4e2d\u5fc3\u5316\u3002\u9ed8\u8ba4\u503c\u4e3aTRUE\u3002<\/span><\/span><\/p>\n\u2022<\/span>crossval<\/span>: \u6307\u793a\u4ea4\u53c9\u9a8c\u8bc1\u6bb5\u6570\u7684\u6574\u6570\u3002\u6837\u672c\u6570\uff08\u201cx\u201d\u7684\u884c\u6570\uff09\u5fc5\u987b\u5927\u4e8e\u7b49\u4e8ecrossvalI\u3002\u5982\u679c\u4e3aNULL\uff08\u9ed8\u8ba4\u503c\uff09\uff0c\u5219\u8fdb\u884cleave-one-out\u4ea4\u53c9\u9a8c\u8bc1\u3002<\/span><\/span><\/p>\n\u2022<\/span>showinfo<\/span>: \u903b\u8f91\u503c\uff0c\u6307\u793a\u662f\u5426\u663e\u793a\u51fd\u6570\u8fdb\u5ea6\u4fe1\u606f\u3002\u9ed8\u8ba4\u503c\u4e3aTRUE\u3002 <\/span>genModelList<\/span>\u7684\u8f93\u51fa\u662f\u4e00\u4e2a\u5e26\u6709\u65b0\u69fd<\/span>PLSmodels<\/span>\u7684<\/span>mbac<\/span>\u5bf9\u8c61\uff0c\u8be5\u69fd\u662f\u4f7f\u7528<\/span>ropls<\/span>\u5305\u83b7\u5f97\u7684PLS\u6a21\u578b\u7684\u5217\u8868\u3002\u8f93\u51fa\u7684\u6bcf\u4e2a\u69fd\u5bf9\u5e94\u4e8e<\/span>ListOfBatches<\/span>\u4e2d\u7684\u4e00\u4e2a\u6279\u6b21\u3002\u5982\u679c\u4e00\u4e2a\u6279\u6b21\u5305\u542b\u591a\u4e2a\u975e\u516c\u5171omic\uff0c\u5219<\/span>genModelList<\/span>\u4e2d\u7684\u201c\u6279\u6b21\u201d\u5143\u7d20\u5c06\u4f9d\u6b21\u5305\u542b\u4e0e\u8be5\u6279\u6b21\u4e2d\u7684\u975e\u516c\u5171omic\u6570\u91cf\u76f8\u7b49\u7684\u5143\u7d20\uff0c\u5373\u6bcf\u4e2a\u975e\u516c\u5171omic\u4e00\u4e2aPLS\u6a21\u578b\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n\u7f3a\u5931Omics\u7684\u9884\u6d4b<\/strong><\/span><\/p>\n\u5229\u7528genModelList\u51fd\u6570\u8f93\u51fa\u4e2d\u7684genMissingOmics\u51fd\u6570\uff0c\u5bf9\u521d\u6b65\u7f3a\u5931\u7684Omics\u8fdb\u884c\u9884\u6d4b\u3002<\/span><\/p>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\">multiBatchDesign <- genMissingOmics(my_mbac_2)<\/span><\/p>\n\u8fd0\u884c<\/span>genMissingOmics<\/span>\u51fd\u6570\u540e\u5f97\u5230\u7684\u7ed3\u679c\u662f\u4e00\u4e2aMultiAssayExperiment\u7ed3\u6784\u5217\u8868\u3002\u5728\u8fd9\u79cd\u60c5\u51b5\u4e0b\uff0c\u6bcf\u4e2a\u6279\u6b21\u90fd\u5305\u542bMultiBaC\u4e2d\u5f15\u5165\u7684\u6240\u6709Omics\u3002\u4f8b\u5982\uff0c\u5982\u679c\u6b63\u5728\u7814\u7a76\u4e24\u4e2a\u6279\u6b21\u201cA\u201d\u548c\u201cB\u201d\uff0c\u5176\u4e2d\u201cA\u201d\u5305\u542b\u201cRNA-seq\u201d\u548c\u201cGRO-seq\u201d\u6570\u636e\uff0c\u800c\u201cB\u201d\u5305\u542b\u201cRNA-seq\u201d\u548c\u201cMetabolomics\u201d\u6570\u636e\uff0c\u5219\u5728\u5e94\u7528<\/span>genMissingOmics<\/span>\u51fd\u6570\u540e\uff0c\u6279\u6b21\u201cA\u201d\u5c06\u5305\u542b\u201cRNA-seq\u201d\uff0c\u201cGRO-seq\u201d\u4ee5\u53ca\u9884\u6d4b\u7684\u201cMetabolomics\u201d\u6570\u636e\u3002<\/span><\/span><\/p>\n\u6279\u6b21\u6548\u5e94\u6821\u6b63<\/strong><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"properties\"><code>my_finalwise_mbac<\/span> <- batchCorrection(my_mbac_2, <\/span><\/span><\/code><code> multiBatchDesign<\/span> = multiBatchDesign, <\/span><\/span><\/code><code> Interaction<\/span> = TRUE, <\/span><\/span><\/code><code> Variability<\/span> = 0.90)<\/span><\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\">\u5982\u524d\u6240\u8ff0\uff0cARSyN\u5bf9\u6570\u636e\u77e9\u9635\u8fdb\u884c\u7c7b\u4f3cANOVA\u7684\u5206\u89e3\uff0c\u4ee5\u4f30\u8ba1\u6279\u6b21\u6548\u5e94\uff0c\u7136\u540e\u5728\u6bcf\u4e2a\u5b50\u77e9\u9635\u4e0a\u5e94\u7528PCA\u3002\u6bcf\u4e2aPCA\u7684\u4e3b\u6210\u5206\u6570\u91cf\u901a\u8fc7\u201cVariability\u201d\u53c2\u6570\u8fdb\u884c\u8c03\u6574\u3002\u8be5\u51fd\u6570\u7684\u8f93\u51fa\u7531\u4e24\u4e2a\u4e0d\u540c\u7684\u5bf9\u8c61\u7ec4\u6210\uff1a<\/span><span style=\"font-size: 15px;letter-spacing: 0.034em;text-align: justify;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;font-style: italic;\">CorrectedData<\/span>\u548c<\/span><span style=\"font-size: 15px;letter-spacing: 0.034em;text-align: justify;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;font-style: italic;\">ARSyNmodels<\/span>\u3002\u524d\u8005\u4e0e\u201cListOfBatches\u201d\u69fd\u7684\u7ed3\u6784\u76f8\u540c\u3002\u7136\u800c\uff0c\u5728\u8fd9\u79cd\u60c5\u51b5\u4e0b\uff0c\u6240\u6709\u6279\u6b21\u90fd\u5305\u542bMultiBaC\u4e2d\u5f15\u5165\u7684\u6240\u6709 omics\uff0c\u8fd9\u662f\u901a\u8fc7\u5bf9\u6bcf\u4e2aomics\u6570\u636e\u7c7b\u578b\u5206\u522b\u8fdb\u884c\u6279\u6b21\u6548\u5e94\u6821\u6b63\u540e\u5f97\u5230\u7684\u3002\u8bf7\u6ce8\u610f\uff0c\u6211\u4eec\u4e22\u5f03\u4e86\u9884\u6d4b\u7684omics\u77e9\u9635\uff0c\u53ea\u5728\u540e\u7eed\u7684\u7edf\u8ba1\u5206\u6790\u4e2d\u4f7f\u7528\u7ecf\u8fc7\u6821\u6b63\u7684\u539f\u59cb\u77e9\u9635\u3002<\/span><span style=\"font-size: 15px;letter-spacing: 0.034em;text-align: justify;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;font-style: italic;\">ARSyNmodels<\/span>\u69fd\u5305\u542b\u6bcf\u4e2aomics\u6570\u636e\u7c7b\u578b\u7684ASCA\u5206\u89e3\u6a21\u578b\u3002<\/span><\/p>\nARSyN\u548cMultiBaC\u7ed3\u679c\u7684\u53ef\u89c6\u5316<\/strong> <\/p>\n\u5982\u524d\u6240\u8ff0\uff0c<\/span>ARSyNbac<\/span>\u548c<\/span>MultiBaC<\/span>\u7684\u8f93\u51fa\u662f<\/span>mbac<\/span>\u7c7b\u578b\u7684\u5bf9\u8c61\u3002\u7531\u4e8e<\/span>mbac<\/span>\u7c7b\u5305\u542b\u7ed8\u56fe\u65b9\u6cd5\uff0c\u56e0\u6b64\u53ef\u4ee5\u5c06<\/span>plot\u51fd\u6570\u5e94\u7528\u4e8e<\/span>mbac<\/span>\u5bf9\u8c61\uff0c\u4ee5\u56fe\u5f62\u65b9\u5f0f\u663e\u793a\u6709\u5173\u65b9\u6cd5\u548c\u6570\u636e\u7279\u5f81\u7684\u6027\u80fd\u7684\u9644\u52a0\u4fe1\u606f\u3002<\/span>mbac<\/span>\u5bf9\u8c61\u7684<\/span>plot*\u51fd\u6570\u63a5\u53d7\u51e0\u4e2a\u989d\u5916\u7684\u53c2\u6570\uff1a<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code>plot (x, typeP = \"def\"<\/span>, <\/span><\/code><code> col.by.batch = TRUE<\/span>, <\/span><\/code><code> col.per.group = NULL<\/span>, <\/span><\/code><code> comp2plot = c(1<\/span>,2<\/span>), <\/span><\/code><code> legend.text = NULL<\/span>, <\/span><\/code><code> args.legend = NULL<\/span>, ...)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\"><span style=\"font-family: mp-quote, -apple-system-font, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Hiragino Sans GB", "Microsoft YaHei UI", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 0.034em;text-align: justify;color: rgb(2, 30, 170);font-size: 15px;\">\u63cf\u8ff0\u53c2\u6570\uff1a <\/strong><\/span><span style=\"font-family: mp-quote, -apple-system-font, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Hiragino Sans GB", "Microsoft YaHei UI", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 0.034em;text-align: justify;font-size: 15px;\"> <\/span><\/p>\n\u2022<\/span>x<\/span>: \u7531<\/span>MultiBaC<\/span>\u65b9\u6cd5\u8fd4\u56de\u7684\u201cmbac\u201d\u7c7b\u5bf9\u8c61\u3002<\/span><\/span><\/p>\n\u2022<\/span>typeP<\/span>: \u8981\u663e\u793a\u7684\u56fe\u5f62\u7684\u7c7b\u578b\u3002\u9009\u9879\u6709\uff1a\u201cdef\u201d \uff08\u9ed8\u8ba4\u9009\u9879\uff0c\u5bf9\u4e8eMultiBaC\u662f\u201cQ2 plot\u201d\u548c\u201cExplained variance plot\u201d\uff0c\u5bf9\u4e8eARSyNbac\u8f93\u51fa\u662f\u201cExplained variance plot\u201d\uff09 \u3001\u201cinner\u201d\uff08\u5bf9\u4e8eMultiBaC\u8f93\u51fa\uff0c\u662f\u6bcf\u4e2aPLS\u6a21\u578b\u7684\u5185\u90e8\u76f8\u5173\u6027\u56fe\uff09\u3001\u201cpca.org\u201d\uff08\u5bf9\u4e8eMultiBaC\u6216ARSyNbac\u8f93\u51fa\uff0c\u662f\u539f\u59cb\u6570\u636e\u7684PCA\u56fe\uff09\u3001\u201cpca.cor\u201d\uff08\u5bf9\u4e8eMultiBaC\u6216ARSyNbac\u8f93\u51fa\uff0c\u662f\u4fee\u6b63\u6570\u636e\u7684PCA\u56fe\uff09\u3001\u201cpca.both\u201d\uff08\u5bf9\u4e8eMultiBaC\u6216ARSyNbac\u8f93\u51fa\uff0c\u662f\u539f\u59cb\u548c\u4fee\u6b63\u6570\u636e\u7684PCA\u56fe\uff09\u4ee5\u53ca\u201cbatch\u201d\uff08\u5bf9\u4e8e\u6240\u6709\u8f93\u51fa\uff0c\u662f\u201cBatch effect estimation\u201d\u56fe\uff09\u3002\u8bf7\u6ce8\u610f\uff0c\u5f53\u6240\u6709omics\u5171\u4eab\u76f8\u540c\u7684\u53d8\u91cf\u7a7a\u95f4\u65f6\uff08\u4f8b\u5982\uff0c\u4e3a\u6240\u6709\u6570\u636e\u77e9\u9635\u63d0\u4f9b\u57fa\u56e0\u6807\u8bc6\u7b26\u4f5c\u4e3a\u53d8\u91cf\u540d\uff09\uff0c\u624d\u80fd\u751f\u6210PCA\u56fe\u3002<\/span><\/span><\/p>\n\u2022<\/span>col.by.batch<\/span>: PCA\u56fe\u7684\u53c2\u6570\u3002TRUE\u6216FALSE\u3002\u5982\u679c\u4e3aTRUE\uff08\u9ed8\u8ba4\uff09\uff0c\u5219\u6837\u672c\u6309\u6279\u6b21\u56e0\u7d20\u7740\u8272\u3002\u5982\u679c\u4e3aFALSE\uff0c\u5219\u6837\u672c\u6309\u5b9e\u9a8c\u6761\u4ef6\u7740\u8272\u3002<\/span><\/span><\/p>\n\u2022<\/span>col.per.group<\/span>: PCA\u56fe\u7684\u53c2\u6570\u3002\u6bcf\u4e2a\u7ec4\u7684\u989c\u8272\uff08\u7531\u6279\u6b21\u6216\u5b9e\u9a8c\u6761\u4ef6\u7ed9\u51fa\uff09\u3002\u5982\u679c\u4e3aNULL\uff08\u9ed8\u8ba4\uff09\uff0c\u5219\u989c\u8272\u4ece\u9884\u5b9a\u4e49\u8c03\u8272\u677f\u4e2d\u9009\u53d6\u3002<\/span><\/span><\/p>\n\u2022<\/span>comp2plot<\/span>: PCA\u6216InnerRel\u56fe\u7684\u53c2\u6570\u3002\u6307\u793a\u8981\u7ed8\u5236\u7684\u7ec4\u4ef6\u3002\u9ed8\u8ba4\u662fc(1,2)\uff0c\u8fd9\u610f\u5473\u7740\u5728PCA\u56fe\u4e2d\uff0c\u7b2c1\u4e2a\u7ec4\u4ef6\u7ed8\u5236\u5728\u201cx\u201d\u8f74\u4e0a\uff0c\u7b2c2\u4e2a\u7ec4\u4ef6\u7ed8\u5236\u5728\u201cy\u201d\u8f74\u4e0a\uff0c\u5bf9\u4e8eInnerRel\u56fe\uff0c\u8981\u663e\u793a\u7b2c1\u548c\u7b2c2\u4e2a\u7ec4\u4ef6\u7684\u5185\u90e8\u5173\u7cfb\u56fe\u3002\u5982\u679c\u6307\u793a\u4e86\u591a\u4e2a\u7ec4\u4ef6\uff0c\u5219\u51fd\u6570\u5c06\u8fd4\u56de\u6240\u9700\u6570\u91cf\u7684\u56fe\u4ee5\u663e\u793a\u6240\u6709\u7ec4\u4ef6\u3002<\/span><\/span><\/p>\n\u2022<\/span>legend.text<\/span>: \u7528\u4e8e\u6784\u9020\u56fe\u4f8b\u7684\u6587\u672c\u5411\u91cf\u3002PCA\u56fe\u7684\u53c2\u6570\u3002\u5982\u679c\u4e3aNULL\uff08\u9ed8\u8ba4\uff09\uff0c\u5219\u4f7f\u7528\u5305\u542b\u5728mbac\u5bf9\u8c61\u4e2d\u7684\u6279\u6b21\u6216\u6761\u4ef6\u540d\u79f0\u3002<\/span><\/span><\/p>\n\u2022<\/span>args.legend<\/span>: legend()\u51fd\u6570\u7684\u9644\u52a0\u53c2\u6570\u5217\u8868\uff1b\u5217\u8868\u4e2d\u7684\u540d\u79f0\u7528\u4f5c\u53c2\u6570\u540d\u79f0\u3002\u4ec5\u5728legend.text\u88ab\u63d0\u4f9b\u65f6\u4f7f\u7528\u3002<\/span><\/span><\/p>\n\u2022<\/span>\u2026<\/span>: \u5176\u4ed6\u56fe\u5f62\u53c2\u6570\u3002 \u867d\u7136 <\/span>plot<\/span> \u51fd\u6570\u53ef\u4ee5\u751f\u6210\u4e0a\u8ff0\u6240\u6709\u7c7b\u578b\u7684\u56fe\uff0c\u4f46\u6bcf\u4e2a\u56fe\u4e5f\u53ef\u4ee5\u901a\u8fc7\u5176\u5bf9\u5e94\u7684\u51fd\u6570\u72ec\u7acb\u751f\u6210\uff0c\u8fd9\u4e9b\u51fd\u6570\u5305\u62ec\uff1a<\/span>Q2_plot (mbac)<\/span>\u3001<\/span>explained_varPlot (mbac)<\/span>\u3001<\/span>plot_pca (mbac, typeP = c(\u201cpca.org\u201d, \u201cpca.cor\u201d, \u201cpca.both\u201d), col.by.batch, col.per.group, comp2plot, legend.text, args.legend)<\/span>\u3001<\/span>batchEstPlot (mbac)<\/span>\u4ee5\u53ca <\/span>inner_relPlot (mbac, comp2plot = c(1,2))<\/span>. \u6240\u6709\u8fd9\u4e9b\u56fe\u90fd\u6709\u52a9\u4e8e\u9a8c\u8bc1\u548c\u7406\u89e3<\/span>MultiBaC<\/span>\u6216<\/span>ARSyNbac<\/span>\u7684\u6027\u80fd\u3002\u6240\u6709\u8fd9\u4e9b\u56fe\u90fd\u53ef\u4ee5\u4f7f\u7528<\/span>MultiBaC<\/span>\u7684\u8f93\u51fa\uff0c\u800c\u663e\u793a\u4e0ePLS\u6a21\u578b\u76f8\u5173\u7684\u4fe1\u606f\u56fe\u5219\u4e0d\u9002\u7528\u4e8e<\/span>ARSyNbac<\/span>\u7684\u8f93\u51fa\uff08\u8bf7\u53c2\u89c1<\/span>typeP<\/span>\u53c2\u6570\uff09\u3002 \u9664\u4e86\u201cQ2 plot\u201d\u548c\u201cExplained variance plot\u201d\uff08\u56fe7\uff09\u662f\u9ed8\u8ba4\u7ed8\u5236\u7684\uff0c\u5e76\u4e14\u5728\u524d\u9762\u90e8\u5206\u4ecb\u7ecd\u8fc7\uff0c\u540e\u9762\u90e8\u5206\u7528\u4e8e\u63cf\u8ff0MultiBaC\u5305\u4e2d\u7684\u5176\u4ed6\u56fe\u8868\u3002<\/span> <\/span><o:page><\/o:page><\/p>\nPLS\u6a21\u578b\u4e2d\u7684\u5185\u90e8\u76f8\u5173\u6027<\/strong><\/span><\/p>\n\u5728MultiBaC\u4e2d\u9700\u8981\u9a8c\u8bc1\u7684\u4e00\u4e2a\u91cd\u8981\u65b9\u9762\u662fPLS\u6a21\u578b\u4e2dX\u548cY\u5206\u6570\u4e4b\u95f4\u7684\u5185\u5728\u76f8\u5173\u6027\u3002\u6b63\u5982\u6211\u4eec\u4e4b\u524d\u6307\u51fa\u7684\u90a3\u6837\uff0c\u300aMultiBaC\u300b\u51fd\u6570\u9ed8\u8ba4\u60c5\u51b5\u4e0b\u4ee5\u6570\u503c\u5f62\u5f0f\u663e\u793a\u6b64\u4fe1\u606f\uff0c\u4f46\u4e5f\u53ef\u4ee5\u8c03\u7528\u53ef\u89c6\u5316\u8868\u793a\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code>plot (my_final_mbac, typeP =\"inner\", comp2plot =c(1,2)) <\/span><\/code><code>#<\/span># Hitto see next plot: <\/span><\/span><\/code><code>#<\/span># Inner correlation of scores. Batch: A; Model for omic: GRO <\/span><\/span><\/code><code>#<\/span># Warning in par(initpar): graphical parameter \"cin\" cannot be set<\/span><\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014473\" data-ratio=\"0.5592592592592592\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_IfhW0DTyX0dKkDlOlP5AhJHRGNBicg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVS3QukpNu5XEY3LnU0XRJiaFkRYxIfhW0DTyX0dKkDlOlP5AhJHRGNBicg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"313.20001220703125\" width=\"560.010009765625\" \/><\/span> <\/span>\u56fe8\uff1a<\/span>PLS\u7ec4\u4ef6\u5185\u90e8\u5173\u7cfb\u7684\u7ed8\u56fe<\/span><\/span><\/p>\n\u4ec5\u4ee5\u6279\u6b21\u201cA\u201d\u4e3a\u4f8b\u663e\u793a\u7ed3\u679c\u3002\u6bcf\u4e2a\u9762\u677f\u8868\u793aPCA\u6a21\u578b\u7684\u4e00\u4e2a\u7ec4\u4ef6\u7684\u5185\u90e8\u76f8\u5173\u6027\u3002\u7ea2\u7ebf\u8868\u793a\u5bf9\u89d2\u7ebf\uff0c\u6b64\u65f6\u76f8\u5173\u6027\u6700\u5927\uff081\uff1a1\uff09\u3002 \u5982\u56fe8\u6240\u793a\uff0cPLS\u6a21\u578b\u4e2d\u4e0e\u201cA\u201d\u6279\u6b21\u4e2d\u4e24\u79cd\u7ec4\u5b66\u6570\u636e\u7c7b\u578b\u5747\u76f8\u5173\u7684\u5185\u90e8\u76f8\u5173\u6027\u5f97\u5206\u3002\u867d\u7136\u6211\u4eec\u4ec5\u5c55\u793a\u4e86\u201cA\u201d\u6279\u6b21\u7684\u6563\u70b9\u56fe\uff0c\u4f46\u901a\u8fc7\u8fd0\u884cplot\uff08typeP = \u201cinner\u201d\uff09\u547d\u4ee4\uff0cMultiBaC\u6027\u80fd\u4e2d\u751f\u6210\u7684PLS\u6a21\u578b\u7684\u6240\u6709\u5185\u90e8\u76f8\u5173\u6027\u56fe\u90fd\u5c06\u4ee5\u201cHit to see next plot:\u201d\u6807\u7b7e\u663e\u793a\uff0c\u56e0\u6b64\u9700\u8981\u7528\u6237\u4ea4\u4e92\u624d\u80fd\u663e\u793a\u5b8c\u6574\u7684\u4e00\u7ec4\u56fe\u5f62\u3002\u6a21\u578b\u7684\u76f8\u5173\u4fe1\u606f\uff08\u5305\u62ec\u6279\u6b21\u548c\u7ec4\u5b66\uff09\u4e5f\u4f1a\u5728R\u63d0\u793a\u7b26\u4e2d\u663e\u793a\u3002\u201c\u5185\u90e8\u76f8\u5173\u6027\u56fe\u201d\u662f\u4e00\u4e2a\u5173\u952e\u7ed3\u679c\uff0c\u56e0\u4e3a\u5b83\u4ee3\u8868\u4e86PLS\u6a21\u578b\u7684\u9a8c\u8bc1\u3002\u5728\u6bcf\u4e2a\u6210\u5206\u4e2d\uff0cx\u5206\u6570\uff08t\uff09\u548cy\u5206\u6570\uff08u\uff09\u4e4b\u95f4\u7684\u76f8\u5173\u6027\u5e94\u8be5\u662f\u7ebf\u6027\u7684\uff0c\u5982\u56fe8\u6240\u793a\u3002\u5982\u679c\u89c2\u5bdf\u5230\u975e\u7ebf\u6027\u76f8\u5173\u6027\uff0c\u5219\u9700\u8981\u5bf9\u6570\u636e\u8fdb\u884c\u8f6c\u6362\u3002 <\/span> <\/span><o:page><\/o:page><\/p>\n\u6279\u6b21\u6548\u5e94\u4f30\u8ba1\u56fe<\/strong><\/span><\/p>\n\u6b64\u56fe\u663e\u793a\u4e86\u4f30\u8ba1\u6279\u6b21\u6548\u5e94\u7684\u5e45\u5ea6\u3002\u901a\u5e38\uff0c\u5728\u6267\u884c<\/span>MultiBaC<\/span>\u6216<\/span>ARSyNbac<\/span>\u4e4b\u524d\u4f7f\u7528\u6b64\u56fe\uff0c\u56e0\u4e3a\u5b83\u53ea\u9700\u8981<\/span>createMbac<\/span>\u51fd\u6570\u8fd4\u56de\u7684<\/span>mbac<\/span>\u57fa\u672c\u6570\u636e\u3002<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code>plot<\/span> (my_final_mbac, typeP =\"batch\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\"><\/span><\/span><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014472\" data-ratio=\"0.5824074074074074\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/12_icW8GYkdyuNhJ3aBfh4eKcqwGBoFkg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSKKWd4reLlMWHAQRHKibpp5xsUQicW8GYkdyuNhJ3aBfh4eKcqwGBoFkg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"326.3999938964844\" width=\"560.010009765625\" \/><\/span> <\/span> \u56fe9\uff1a<\/span>\u6279\u6b21\u6548\u5e94\u4f30\u8ba1\u56fe<\/span><\/span><\/p>\n<p style=\"margin-top: 9.0pt;margin-bottom: 9.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\">\u865a\u7ebf\u8868\u793a\u7406\u8bba\u6279\u6b21\u6548\u5e94\u5e45\u5ea6\u3002\u5c0f\u63d0\u7434\u56fe\u8868\u793a\u6570\u636e\u4e2d\u89c2\u5bdf\u5230\u7684\u6279\u6b21\u6548\u5e94\u7cfb\u6570\u7684\u5206\u5e03\u3002 \u9175\u6bcd\u4f8b\u5b50\u7684\u7406\u8bba\u6279\u6b21\u6548\u5e94\u5e45\u5ea6\u5728\u56fe <\/span>9<\/span> \u4e2d\u5c55\u793a\u3002\u5c0f\u63d0\u7434\u56fe\u5c55\u793a\u4e86\u53d8\u91cf\u7a7a\u95f4\u4e2d\u6279\u6b21\u6548\u5e94\u7cfb\u6570\u7684\u5206\u5e03\u60c5\u51b5\uff08\u5bf9\u4e8eRNA-seq\u6570\u636e\u800c\u8a00\uff0c\u8fd9\u4e9b\u53d8\u91cf\u662f\u57fa\u56e0\uff09\u3002\u5177\u6709\u8f83\u9ad8\u503c\u7684\u7cfb\u6570\u5bf9\u5e94\u4e8e\u5bf9\u6279\u6b21\u6548\u5e94\u7684\u5b58\u5728\u8d21\u732e\u6700\u5927\u7684\u90a3\u4e9b\u53d8\u91cf\uff0c\u56e0\u6b64\uff0c\u5f53\u5206\u5e03\u63a5\u8fd1\u96f6\u65f6\uff0c\u6279\u6b21\u6548\u5e94\u8f83\u4f4e\u3002\u5c3d\u7ba1\u5728\u5c0f\u81f3\u4e2d\u7b49\u6279\u6b21\u6548\u5e94\u5e45\u5ea6\u4e0b\uff0cMultiBaC\u7684\u4fee\u6b63\u6027\u80fd\u5df2\u7ecf\u8fc7\u6d4b\u8bd5\u548c\u9a8c\u8bc1\uff0c\u4f46\u5728\u5927\u6279\u91cf\u6548\u5e94\u4e0b\u5176\u6027\u80fd\u6709\u6240\u4e0b\u964d\u3002\u76f8\u6bd4\u4e4b\u4e0b\uff0cARSyN\u53d7\u6279\u6b21\u6548\u5e94\u5e45\u5ea6\u7684\u5f71\u54cd\u5e76\u4e0d\u5927\u3002 \u4ee5\u4e0b\u662fPCA\u56fe\u8868\u7684\u4e2d\u6587\u7ffb\u8bd1\u3002<\/span> <\/span><o:page><\/o:page><\/p>\nPCA\u56fe<\/strong><\/span><\/p>\n\u53ef\u4ee5\u901a\u8fc7\u6bd4\u8f83\u4fee\u6b63\u524d\u540e\u7684PCA\u56fe\u6765\u8bc4\u4f30<\/span>ARSyNbac<\/span>\u6216<\/span>MultiBaC<\/span>\u4fee\u6b63\u7684\u6548\u679c\u3002\u5bf9\u4e8e<\/span>MultiBaC<\/span>\uff0c\u53ea\u6709\u5728\u6240\u6709\u7ec4\u5b66\u6570\u636e\u77e9\u9635\u5171\u4eab\u76f8\u540c\u7684\u53d8\u91cf\u7a7a\u95f4\u65f6\uff0c\u624d\u80fd\u751f\u6210\u8fd9\u79cd\u56fe\u3002\u5728\u6211\u4eec\u63d0\u4f9b\u7684\u9175\u6bcd\u793a\u4f8b\u4e2d\uff0c\u6bcf\u79cd\u7ec4\u5b66\u6570\u636e\u7c7b\u578b\u90fd\u662f\u4ee5\u57fa\u56e0\u76f8\u5173\u4fe1\u606f\u7684\u5f62\u5f0f\u83b7\u5f97\u7684\uff0c\u56e0\u6b64\u53ef\u4ee5\u5c06\u77e9\u9635\u6309\u53d8\u91cf\uff08\u57fa\u56e0\uff09\u5408\u5e76\uff0c\u8fdb\u884cPCA\u5206\u6790\u3002 \u8fd9\u4e9bPCA\u56fe\u5bf9\u4e8e<\/span>ARSyNbac<\/span>\u8f93\u51fa\u7684\u793a\u4f8b\u53ef\u4ee5\u5728ARSyN\u90e8\u5206\u627e\u5230\u3002\u8fd9\u91cc\u6211\u4eec\u6f14\u793a\u4e86\u5982\u4f55\u751f\u6210\u548c\u89e3\u91ca\u5b83\u4eec\u4ee5\u8fdb\u884cMultiBaC\u6821\u6b63\u3002\u5728\u539f\u59cb\u6570\u636e\u4e0a\u7684PCA\uff08\u56fe10\uff1a\u3010\u94fe\u63a5\u3011\uff09\u548c\u6821\u6b63\u6570\u636e\u4e0a\u7684PCA\uff08\u56fe11\uff1a\u3010\u94fe\u63a5\u3011\uff09\u662f\u4f7f\u7528plot\u51fd\u6570\u83b7\u5f97\u7684\uff0c\u5206\u522b\u4f7f\u7528<\/span>\u201ctypeP = pca.org\u201d<\/span>\u6216<\/span>\u201ctypeP = pca.cor\u201d<\/span>\u3002<\/span><\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code>plot<\/span> (my_final_mbac, typeP =\"pca.org\"<\/span>, <\/span><\/code><code> cex.axis =1<\/span>, cex.lab =1<\/span>, cex =3<\/span>, bty =\"L\"<\/span>, <\/span><\/code><code> cex.main =1<\/span>.2<\/span>, pch =19<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\"><\/span><\/span><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014475\" data-ratio=\"0.5555555555555556\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/13_UXNqveDbThx0cwNOdHed6SKvkv1XJA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSCJ07UJYLiaJPjuuXLg51oibQNzUXNqveDbThx0cwNOdHed6SKvkv1XJA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"311.2000427246094\" width=\"560.010009765625\" \/><\/span> <\/span>\u56fe10\uff1a<\/span>\u5728\u539f\u59cb\u6570\u636e\u4e0a\u6267\u884cPCA\u5f97\u5230\u7684\u4e3b\u6210\u5206\u56fe<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code>plot<\/span> (my_final_mbac, typeP =\"pca.cor\"<\/span>, <\/span><\/code><code> cex.axis =1<\/span>, cex.lab =1<\/span>, cex =3<\/span>, bty =\"L\"<\/span>, <\/span><\/code><code> cex.main =1<\/span>.2<\/span>, pch =19<\/span>) <\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\"> <\/span><o:page><\/o:page><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014474\" data-ratio=\"0.5564814814814815\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/14_OlPLykdqXG3BUknUz5822jP9ibS8WA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSZZaOdq1KlHWv5zjZcb0zoN7ejOlPLykdqXG3BUknUz5822jP9ibS8WA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"311.6000061035156\" width=\"560.010009765625\" \/><\/span> <\/span>\u56fe11\uff1a\u4fee\u6b63\u6570\u636e\u4e0a\u7684\u4e3b\u6210\u5206\u5206\u6790\uff08PCA\uff09\u56fe\uff08\u9ed8\u8ba4\u8bbe\u7f6e)<\/span><\/p>\n\u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff0c\u6b64\u51fd\u6570\u4f7f\u7528\u968f\u673a\u989c\u8272\u8868\u793a\u6bcf\u4e2a\u7ec4\uff08\u9ed8\u8ba4\u60c5\u51b5\u4e0b\u662f\u6279\u6b21\uff09\u3002\u7136\u800c\uff0c\u540c\u65f6\u663e\u793a\u5b9e\u9a8c\u56e0\u7d20\u4fe1\u606f\u4f1a\u5f88\u6709\u7528\u3002\u4e3a\u6b64\uff0c\u6211\u4eec\u5efa\u8bae\u4f7f\u7528\u81ea\u5b9a\u4e49\u7684<\/span>col.per.group<\/span>\u548c<\/span>pch<\/span>\u53c2\u6570\u3002\u56fe<\/span><\/span>12<\/span>\u4e2d\u7ed9\u51fa\u4e86\u4e00\u4e2a\u793a\u4f8b\uff0c\u4f7f\u7528typeP = pca.both\u540c\u65f6\u663e\u793a\u4e24\u4e2aPCA\u56fe\u3002\u6211\u4eec\u8fd8\u53ef\u4ee5\u4f7f\u7528<\/span>comp2plot<\/span>\u53c2\u6570\u7ed8\u5236\u591a\u4e2a\u7ec4\u4ef6\uff0c\u4ee5\u6307\u793a\u6240\u9700\u6570\u91cf\u3002\u7528\u6237\u8fd8\u53ef\u4ee5\u4f7f\u7528\u4e24\u4e2a\u53c2\u6570\u6dfb\u52a0\u81ea\u5b9a\u4e49\u56fe\u4f8b\uff1a<\/span>legend.text<\/span>\u548c<\/span>args.legend<\/span>\u3002\u901a\u8fc7<\/span>legend.text<\/span>\uff0c\u6211\u4eec\u6307\u793a\u56fe\u4f8b\u7684\u6587\u672c\u6807\u7b7e\uff0c\u5176\u4f59\u56fe\u4f8b\u53c2\u6570\u4fdd\u5b58\u5728<\/span>args.legend<\/span>\uff08x\uff0cy\uff0cpch\uff0cfill\uff0ccol\uff0cbty\u7b49)\u4e2d\u3002\u5982\u679c\u5411\u51fd\u6570\u63d0\u4f9b<\/span>legend.text<\/span>\uff0c\u5219\u4e0d\u8003\u8651<\/span>args.legend<\/span>\u3002<\/span><\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code>custom_col <-c(\"brown2\"<\/span>, \"dodgerblue\"<\/span>, \"forestgreen\"<\/span>) <\/span><\/code><code>custom_pch <-c(19<\/span>,19<\/span>,19<\/span>,1<\/span>,1<\/span>,1<\/span>,15<\/span>,15<\/span>,15<\/span>,0<\/span>,0<\/span>,0<\/span>, # batch A <\/span><\/span><\/code><code> 19<\/span>,19<\/span>,1<\/span>,1<\/span>,17<\/span>,17<\/span>,2<\/span>,2<\/span>, # batch B <\/span><\/span><\/code><code> 19<\/span>,19<\/span>,1<\/span>,1<\/span>,18<\/span>,18<\/span>,5<\/span>,5<\/span>) # batch C <\/span><\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>plot(my_final_mbac, typeP =\"pca.both\"<\/span>, col.by.batch =TRUE<\/span>, <\/span><\/code><code> col.per.group = custom_col, comp2plot =1<\/span>:3<\/span>, <\/span><\/code><code> cex.axis =1.3<\/span>, cex.lab =1.2<\/span>, cex =3<\/span>, bty =\"L\"<\/span>, <\/span><\/code><code> cex.main =1.7<\/span>, pch = custom_pch, <\/span><\/code><code> legend.text =c(\"Color\"<\/span>, names(my_final_mbac$ListOfBatches), <\/span><\/code><code> \"Shape\"<\/span>, c(\"RNA\"<\/span>, \"GRO\"<\/span>, \"RIBO\"<\/span>, \"PAR\"<\/span>), <\/span><\/code><code> \"Fill\"<\/span>, levels(colData(my_final_mbac$ListOfBatches$A)$tfactor)), <\/span><\/code><code> args.legend =list<\/span>(\"x\"<\/span>=\"topright\"<\/span>, <\/span><\/code><code> \"pch\"<\/span>=c(NA, 15<\/span>, 15<\/span>, 15<\/span>, <\/span><\/code><code> NA, 19<\/span>, 15<\/span>, 17<\/span>, 18<\/span>, <\/span><\/code><code> NA, 19<\/span>, 1<\/span>), <\/span><\/code><code> \"col\"<\/span>=c(NA, \"brown2\"<\/span>, \"dodgerblue\"<\/span>, \"forestgreen\"<\/span>, <\/span><\/code><code> NA, rep(1<\/span>, 4<\/span>), <\/span><\/code><code> NA, 1<\/span>, 1<\/span>), <\/span><\/code><code> \"bty\"<\/span>=\"n\"<\/span>, <\/span><\/code><code> \"cex\"<\/span>=2<\/span>)) <\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014476\" data-ratio=\"0.7888888888888889\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/15_AwWHqpCqekDhpGrzITvdXsNbwRjpdw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSVew362JosFQgq2EWer01n6qAAwWHqpCqekDhpGrzITvdXsNbwRjpdw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"442.0099792480469\" width=\"560.010009765625\" \/><\/span> <\/span>\u56fe12\uff1a<\/span>\u5b9a\u5236\u7684\u4e3b\u6210\u5206\u5206\u6790\u56fe<\/span><\/span><\/p>\n\u539f\u59cb\u6570\u636e\uff08\u5de6\u4fa7\u9762\u677f\uff09\u548c\u4fee\u6b63\u6570\u636e\uff08\u53f3\u4fa7\u9762\u677f\uff09\u3002\u4e0a\u56fe\u663e\u793a\u7b2c\u4e8c\u4e3b\u6210\u5206\uff08PC\uff09\u4e0e\u7b2c\u4e00\u4e3b\u6210\u5206\u7684\u5173\u7cfb\uff0c\u800c\u4e0b\u56fe\u5219\u663e\u793a\u7b2c\u4e09\u4e3b\u6210\u5206\u4e0e\u7b2c\u4e00\u4e3b\u6210\u5206\u7684\u5173\u7cfb\u3002 \u5728\u8fd9\u79cd\u60c5\u51b5\u4e0b\uff0c\u6279\u6b21\u6548\u5e94\u6821\u6b63\u53ef\u5728\u901a\u7528\u6570\u636e\uff08RNA-seq\u3001\u70b9\uff09\u4e2d\u89c2\u5bdf\u5230\u3002\u5f53\u901a\u7528\u6570\u636e\u653e\u5728\u4e00\u8d77\u540e\uff0c\u6279\u6b21\u6548\u5e94\u5df2\u88ab\u79fb\u9664\uff0c\u5e76\u4e14\u5728\u6821\u6b63\u540e\uff0c\u8fd9\u4e9b\u6210\u5206\uff08\u5c24\u5176\u662f\u7b2c\u4e8c\u548c\u7b2c\u4e09\u6210\u5206)\u4f1a\u6839\u636e\u5b9e\u9a8c\u6761\u4ef6\u5bf9\u901a\u7528\u6570\u636e\u8fdb\u884c\u5206\u79bb\uff0c\u800c\u4e0d\u662f\u6839\u636e\u6279\u6b21\u8fdb\u884c\u5206\u79bb\u3002\u5982\u56fe\u4f8b\u6240\u793a\uff0c\u70b9\u7684\u5f62\u72b6\u8868\u793a omic\u6570\u636e\u7c7b\u578b\uff0c\u7136\u800c\u6279\u6b21\u6548\u5e94\u6821\u6b63\u4ec5\u5728\u901a\u7528\u6570\u636e\u4e2d\u53ef\u89c1\u3002<\/span><\/span><\/p>\n\u603b\u7ed3<\/strong><\/span><\/p>\nMultiBaC\u662f\u7528\u4e8e\u591a\u7ec4\u5b66\u548c\u9690\u85cf\u6279\u6b21\u6548\u5e94\u573a\u666f\u4e2d\u7684\u6279\u91cf\u6548\u5e94\u53bb\u9664\u5de5\u5177\u3002\u8be5\u5305\u63d0\u4f9b\u591a\u79cd\u56fe\u5f62\u8f93\u51fa\uff0c\u7528\u4e8e\u6a21\u578b\u9a8c\u8bc1\u548c\u6279\u91cf\u6548\u5e94\u6821\u6b63\u8bc4\u4f30\u3002\u5feb\u548c\u5c0f\u679c\u4e00\u8d77\u7528MultiBaC R\u5305\u66f4\u6709\u6548\u5730\u5904\u7406\u591a\u7ec4\u5b66\u5b9e\u9a8c\u4e2d\u7684\u6279\u91cf\u6548\u5e94\u95ee\u9898\uff0c\u4ece\u800c\u63d0\u9ad8\u6570\u636e\u5206\u6790\u7684\u51c6\u786e\u6027\u548c\u53ef\u9760\u6027\u5427\uff01<\/span> <\/span><o:page><\/o:page><\/p>\n\u53c2\u8003\u6587\u732e<\/strong><\/span><\/p>\n1.Nueda MJ, Ferrer A, Conesa A. ARSyN: A method for the identification and removal of systematic noise in multifactorial time course microarray experiments. Biostatistics. 2012;13:553\u201366.<\/span><\/p>\n2.Pelechano V, P\u00e9rez-Ort\u00edn JE. There is a steady-state transcriptome in exponentially growing yeast cells. Yeast. 2010;27:413\u201322. doi:<\/span>10.1002\/yea.1768<\/span>.<\/span><\/p>\n3.Garc\u00eda-Mart\u00ednez J, Aranda A, P\u00e9rez-Ort\u00edn J. Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Molecular Cell. 15:303\u201313. doi:<\/span>10.1016\/j.molcel.2004.06.004<\/span>.<\/span><\/p>\n4.Pelechano V, Ch\u00e1vez S, P\u00e9rez-Ort\u00edn JE. A complete set of nascent transcription rates for yeast genes. PloS one. 5:e15442; e15442\u20132. doi:<\/span>10.1371\/journal.pone.0015442<\/span>.<\/span><\/p>\n5.Zid BM, O\u2019Shea EK. Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast. Nature. 514:117\u201321. doi:<\/span>10.1038\/nature13578<\/span>.<\/span><\/p>\n6.Freeberg MA, Han T, Moresco JJ, Kong A, Yang Y-C, Lu ZJ, et al. Pervasive and dynamic protein binding sites of the mRNA transcriptome in saccharomyces cerevisiae. Genome biology. 14:R13\u20133. doi:<\/span>10.1186\/gb-2013-14-2-r13<\/span>.<\/span><\/p>\n<section powered-by=\"xiumi.us\" style=\"margin-bottom: 0px;\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100014478\" data-ratio=\"0.5555555555555556\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/16_VmRkv7tSNKliafDnsuFR7BoeDgBrww.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAxPqeNQsFjm2HibIuSld9Nh9GicQSWhJwHjia5tEevQvDIebLErVmRkv7tSNKliafDnsuFR7BoeDgBrww\/640?wx_fmt=jpeg&from=appmsg'\" data-type=\"jpeg\" data-w=\"900\" style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\" \/> <\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"margin-top: 0pt;margin-bottom: 0pt;margin-left: 0pt;letter-spacing: 0.578px;text-indent: 0pt;text-wrap: wrap;text-align: justify;line-height: normal;font-size: 12pt;font-family: helvetica;color: rgb(0, 0, 0);break-after: auto;\"><\/span><\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;color: rgba(0, 0, 0, 0.9);font-family: mp-quote, -apple-system-font, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Hiragino Sans GB", "Microsoft YaHei UI", "Microsoft YaHei", Arial, sans-serif;text-align: justify;\"><\/span><img decoding=\"async\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014477\" data-ratio=\"0.38981481481481484\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/17_FbEg9fibwQicL8l2ExKOZZTmAHXabQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAx3HetBkB7aOGibFWKqibqIATyC4zFibzCgdrxFwRep6cDMLIbA0FbEg9fibwQicL8l2ExKOZZTmAHXabQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;caret-color: rgba(0, 0, 0, 0);\" \/><\/span><\/p>\n<section powered-by=\"xiumi.us\" style=\"margin-bottom: 0px;letter-spacing: 0.578px;text-wrap: wrap;outline: 0px;font-family: system-ui, -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Hiragino Sans GB", "Microsoft YaHei UI", "Microsoft YaHei", Arial, sans-serif;background-color: rgb(255, 255, 255);text-align: left;\">\n<section style=\"outline: 0px;font-size: 16px;\">\n<section powered-by=\"xiumi.us\" style=\"margin: 10px;outline: 0px;justify-content: flex-start;display: flex;flex-flow: row;\">\n<section style=\"padding-right: 10px;padding-left: 10px;outline: 0px;display: inline-block;width: 558px;vertical-align: top;border-style: 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href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2821072943068839938#wechat_redirect\" title=\"\u751f\u4fe1\u7ed8\u56fe\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u7ed8\u56fe<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2664545260517294084#wechat_redirect\" title=\"\u751f\u4fe1\u5b9e\u64cd\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5b9e\u64cd<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=3138206666342268940#wechat_redirect\" title=\"\u751f\u4fe1\u5c0f\u767d\u76f8\u5173\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5c0f\u767d\u76f8\u5173<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=3138222091851530242#wechat_redirect\" title=\"\u751f\u4fe1\u6709\u5173\u7edf\u8ba1\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u6709\u5173\u7edf\u8ba1<\/a><\/p>\n<\/div>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100014483\" data-ratio=\"0.23333333333333334\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_rE2v0O5WiaUDJjgv5bxK2G1ePHyH2g-40.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAysHY49vPGCraibakiaNq6hQgn8C5MfvVLQGxlNZPEia2PajKAzrE2v0O5WiaUDJjgv5bxK2G1ePHyH2g\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"letter-spacing: 0.578px;text-wrap: wrap;font-family: \u5b8b\u4f53;font-size: 15px;text-align: center;\">\u5728\u751f\u7269\u4fe1\u606f\u5b66\u9886\u57df\uff0c\u968f\u7740\u6280\u672f\u7684\u53d1\u5c55\uff0c\u8d8a\u6765\u8d8a\u591a\u7684\u7814\u7a76\u8005\u5f00\u59cb\u5173\u6ce8\u591a\u7ec4\u5b66\u5b9e\u9a8c\u3002\u7136\u800c\uff0c\u591a\u7ec4\u5b66\u6570\u636e\u4e2d\u5f80\u5f80\u5b58\u5728\u6279\u6b21\u6548\u5e94\uff0c\u8fd9\u4f1a\u5bfc\u81f4\u6280\u672f\u566a\u58f0\u63a9\u76d6\u751f\u7269\u5b66\u4fe1\u53f7\uff0c\u4ece\u800c\u5f71\u54cd\u6570\u636e\u5206\u6790\u3002\u5c3d\u7ba1\u5df2\u6709\u9488\u5bf9\u5355\u4e2a\u7ec4\u5b66\u6280\u672f\u7684\u6279\u91cf\u6548\u5e94\u53bb\u9664\u65b9\u6cd5\uff0c\u4f46\u591a\u7ec4\u5b66\u6570\u636e\u96c6\u53ef\u80fd\u6d89\u53ca\u4e0d\u540c\u6279\u6b21\u7684\u6570\u636e\uff0c\u8fd9\u4f7f\u5f97\u7ec4\u5b66\u7c7b\u578b\u548c\u6279\u6b21\u96be\u4ee5\u533a\u5206\u3002\u6b64\u5916\uff0c\u5728\u6570\u636e\u91c7\u96c6\u8fc7\u7a0b\u4e2d\u53ef\u80fd\u5b58\u5728\u7cfb\u7edf\u504f\u5dee\uff0c\u5bfc\u81f4\u9690\u85cf\u7684\u6279\u6b21\u6548\u5e94\u3002\u56e0\u6b64\uff0c\u6211\u4eec\u9700\u8981\u4e00\u79cd\u80fd\u591f\u5e94\u5bf9\u8fd9\u4e9b\u6311\u6218\u7684\u65b9\u6cd5\u3002<\/span><\/p>\n\u5c0f\u679c\u5c06\u4ecb\u7ecd\u4e00\u6b3e2022\u5e744\u670828\u65e5\u53d1\u8868\u4e8ebioinformatics\u4e0a\u540d\u4e3aMultiBaC\u7684R\u5305\uff0c\u5b83\u662f\u7528\u4e8e\u591a\u7ec4\u5b66\u548c\u9690\u85cf\u6279\u6b21\u6548\u5e94\u573a\u666f\u4e2d\u7684\u6279\u91cf\u6548\u5e94\u53bb\u9664\u5de5\u5177\u3002\u8be5\u5305\u63d0\u4f9b\u591a\u79cd\u56fe\u5f62\u8f93\u51fa\uff0c\u7528\u4e8e\u6a21\u578b\u9a8c\u8bc1\u548c\u6279\u91cf\u6548\u5e94\u6821\u6b63\u8bc4\u4f30\u3002\u901a\u8fc7\u4f7f\u7528MultiBaC R\u5305\uff0c\u7814\u7a76\u4eba\u5458\u53ef\u4ee5\u66f4\u6709\u6548\u5730\u5904\u7406\u591a\u7ec4\u5b66\u5b9e\u9a8c\u4e2d\u7684\u6279\u91cf\u6548\u5e94\u95ee\u9898\uff0c\u4ece\u800c\u63d0\u9ad8\u6570\u636e\u5206\u6790\u7684\u51c6\u786e\u6027\u548c\u53ef\u9760\u6027\u3002<\/span><\/p>\n <img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014466\" data-ratio=\"0.28888888888888886\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_ZWS5buJa7Hq9Rkvf1VtbnXgInLmQKw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSWyYoB8tjIhBJt5iaa7sjwanulZWS5buJa7Hq9Rkvf1VtbnXgInLmQKw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"161.54000854492188\" width=\"560.010009765625\"><\/p>\n\u7b80\u4ecb<\/span><\/strong><\/span><o:page><\/o:page><\/p>\n\u540c\u65f6\u5bf9\u540c\u4e00\u5206\u5b50\u7cfb\u7edf\u8fdb\u884c\u591a\u7ec4\u5b66\u6d4b\u91cf\uff08\u4f8b\u5982\u8f6c\u5f55\u7ec4\u5b66\u3001\u4ee3\u8c22\u7ec4\u5b66\u3001\u86cb\u767d\u8d28\u7ec4\u5b66\u6216\u8868\u89c2\u57fa\u56e0\u7ec4\u5b66\uff09\uff0c\u5728\u4e00\u9879\u7279\u5b9a\u7814\u7a76\u4e2d\u5e76\u4e0d\u603b\u662f\u53ef\u80fd\u3002\u56e0\u6b64\uff0c\u7814\u7a76\u4eba\u5458\u6709\u65f6\u4f1a\u7ed3\u5408\u4e0d\u540c\u5b9e\u9a8c\u5ba4\u6216\u4e0d\u540c\u6279\u6b21\u4ea7\u751f\u7684\u517c\u5bb9\u6570\u636e\u3002\u5728\u8fd9\u79cd\u60c5\u51b5\u4e0b\uff0c\u6570\u636e\u901a\u5e38\u4f1a\u53d7\u5230\u4e0e\u5b9e\u9a8c\u4e8b\u4ef6\uff08\u5b9e\u9a8c\u5ba4\u3001\u6279\u6b21\u3001\u6280\u672f\u7b49\uff09\u76f8\u5173\u7684\u4e0d\u5fc5\u8981\u5f71\u54cd\uff0c\u5c24\u5176\u662f\u5728\u9ad8\u901a\u91cf\u5206\u5b50\u6d4b\u5b9a\u7684\u60c5\u51b5\u4e0b\uff0c\u8fd9\u53ef\u80fd\u4f1a\u5bfc\u81f4\u566a\u97f3\u4e25\u91cd\u6c61\u67d3\u751f\u7269\u4fe1\u53f7\u3002\u8fd9\u79cd\u4e0d\u5fc5\u8981\u7684\u53d8\u5f02\u6e90\u901a\u5e38\u88ab\u79f0\u4e3a\u201c\u6279\u6b21\u6548\u5e94\u201d\uff0c\u5e76\u4e14\u7ecf\u5e38\u662f\u7ec4\u5b66\u6570\u636e\u96c6\u4e2d\u7684\u7b2c\u4e00\u4e2a\u53d8\u5f02\u6e90\uff0c\u4e0e\u7814\u7a76\u5b9e\u9a8c\u6761\u4ef6\u76f8\u6bd4\u66f4\u4e3a\u7a81\u51fa\u3002 \u90a3\u4e48\uff0c\u4e3a\u4e86\u4ece\u7edf\u8ba1\u5206\u6790\u4e2d\u83b7\u5f97\u6709\u610f\u4e49\u7684\u7ed3\u679c\uff0c\u6d88\u9664\u6279\u6b21\u6548\u5e94\u5c31\u662f\u5fc5\u8981\u7684\u3002\u5982\u679c\u7ec4\u5b66\u5b9e\u9a8c\u8bbe\u8ba1\u5f97\u5f53\uff0c\u6279\u6b21\u6548\u5e94\u4e0e\u611f\u5174\u8da3\u7684\u6548\u5e94\uff08\u5904\u7406\u3001\u75be\u75c5\u3001\u7ec6\u80de\u7c7b\u578b\u7b49\uff09\u4e0d\u76f8\u6df7\u6dc6\uff0c\u6240\u8c13\u7684\u6279\u6b21\u6548\u5e94\u4fee\u6b63\u7b97\u6cd5\uff08BECAs\uff09\u53ef\u4ee5\u7528\u6765\u6d88\u9664\u6216\u81f3\u5c11\u51cf\u8f7b\u7cfb\u7edf\u504f\u5dee\u3002\u56e0\u6b64\uff0c\u8fd9\u4e9b\u65b9\u6cd5\u5bf9\u4e8e\u6574\u5408\u6765\u81ea\u4e0d\u540c\u5b9e\u9a8c\u5ba4\u7684\u6570\u636e\u6216\u5728\u4e0d\u540c\u65f6\u95f4\u6d4b\u91cf\u7684\u6570\u636e\u975e\u5e38\u6709\u7528\u3002\u8fd9\u4e9bBECAs\u4e4b\u4e00\u662fARSyN\u65b9\u6cd5 [<\/span>1<\/span>]\uff0c\u5b83\u4f9d\u8d56\u4e8eANOVA-Simultaneous Components Analysis (ASCA)\u6846\u67b6\u5c06\u7ec4\u5b66\u4fe1\u53f7\u5206\u89e3\u4e3a\u5b9e\u9a8c\u6548\u5e94\u548c\u5176\u4ed6\u4e0d\u9700\u8981\u7684\u6548\u5e94\u3002ARSyN\u5e94\u7528\u4e3b\u6210\u5206\u5206\u6790\uff08PCA\uff09\u6765\u4f30\u8ba1\u7531\u6279\u6b21\u6548\u5e94\u5f15\u8d77\u7684\u7cfb\u7edf\u53d8\u5316\uff0c\u7136\u540e\u4ece\u539f\u59cb\u6570\u636e\u4e2d\u5c06\u5176\u53bb\u9664\u3002 BECAs\u4f20\u7edf\u4e0a\u5e94\u7528\u4e8e\u6d88\u9664\u76f8\u540c\u7c7b\u578b\u7ec4\u5b66\u6570\u636e\u4e2d\u7684\u6279\u6b21\u6548\u5e94\uff0c\u4f8b\u5982\u57fa\u56e0\u8868\u8fbe\u3002\u7136\u800c\uff0c\u7528\u9002\u5f53\u7684\u5b9e\u9a8c\u8bbe\u8ba1\u4ece\u5355\u4e00\u7c7b\u578b\u7684\u7ec4\u5b66\u6570\u636e\u4e2d\u6d88\u9664\u6279\u6b21\u6548\u5e94\u76f8\u5bf9\u7b80\u5355\uff0c\u4f46\u5728\u5904\u7406\u591a\u7ec4\u5b66\u6570\u636e\u96c6\u65f6\u53ef\u80fd\u53d8\u5f97\u4e0d\u53ef\u884c\u3002\u5728\u591a\u7ec4\u5b66\u60c5\u51b5\u4e0b\uff0c\u6bcf\u4e2a\u7ec4\u5b66\u6a21\u6001\u53ef\u80fd\u7531\u4e0d\u540c\u7684\u5b9e\u9a8c\u5ba4\u6216\u5728\u4e0d\u540c\u7684\u65f6\u95f4\u70b9\u6d4b\u91cf\uff0c\u56e0\u6b64\u662f\u5728\u4e0d\u540c\u7684\u6279\u6b21\u4e2d\u83b7\u5f97\u7684\u3002\u5728\u8fd9\u79cd\u60c5\u51b5\u4e0b\uff0c\u6279\u6b21\u6548\u5e94\u4f1a\u4e0e\u201c\u7ec4\u5b66\u7c7b\u578b\u6548\u5e94\u201d\u6df7\u6dc6\uff0c\u65e0\u6cd5\u4ece\u6570\u636e\u4e2d\u79fb\u9664\u3002\u7136\u800c\uff0c\u5728\u67d0\u4e9b\u60c5\u51b5\u4e0b\uff0c\u591a\u7ec4\u5b66\u6279\u6b21\u6548\u5e94\u53ef\u4ee5\u5f97\u5230\u7ea0\u6b63\u3002MultiBaC\u662f\u7b2c\u4e00\u4e2a\u5904\u7406\u591a\u7ec4\u5b66\u6570\u636e\u96c6\u4e2d\u6279\u6b21\u6548\u5e94\u7ea0\u6b63\u7684BECA\u3002MultiBaC\u53ef\u4ee5\u6d88\u9664\u4e0d\u540c\u7ec4\u5b66s\u7684\u6279\u6b21\u6548\u5e94\uff0c\u524d\u63d0\u662f\u81f3\u5c11\u6709\u4e00\u79cd\u5e38\u89c1\u7684\u7ec4\u5b66\u6570\u636e\u7c7b\u578b\u5305\u542b\u5728\u6240\u6709\u6279\u6b21\u4e2d\u3002 <\/span>MultiBaC<\/span>\u5305\u5305\u542b\u4e24\u4e2aBECAs\uff1a\u7528\u4e8e\u4ece\u5355\u4e2a\u7ec4\u5b66\u6570\u636e\u7c7b\u578b\u4e2d\u6821\u6b63\u6279\u6b21\u6548\u5e94\u7684ARSyN\u65b9\u6cd5\u548c\u5904\u7406\u591a\u7ec4\u5b66\u6d4b\u5b9a\u6279\u6b21\u6548\u5e94\u95ee\u9898\u7684MultiBac\u65b9\u6cd5\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n\u5355\u4e2a\u7ec4\u5b66\u6570\u636e\u6279\u6b21\u6548\u5e94\u7684\u4fee\u6b63<\/strong><\/span><\/p>\n\u5173\u4e8eARSyN<\/strong><\/span><\/p>\nARSyN\u65b9\u6cd5\u6982\u8ff0<\/span><\/p>\nARSyN\uff08ASCA\u7cfb\u7edf\u6027\u566a\u58f0\u53bb\u9664\uff09\u662f\u4e00\u79cd\u7ed3\u5408\u4e86\u65b9\u5dee\u5206\u6790\uff08ANOVA\uff09\u548c\u4e3b\u6210\u5206\u5206\u6790\uff08PCA\uff09\u7684\u65b9\u6cd5\uff0c\u7528\u4e8e\u4ece\u4f30\u8ba1\u7684ANOVA\u6a21\u578b\u4e2d\u9274\u5b9a\u51fa\u7ed3\u6784\u53d8\u5f02\uff0c\u8fd9\u4e9b\u6a21\u578b\u9488\u5bf9\u7684\u662f\u5b9e\u9a8c\u548c\u4e0d\u9700\u8981\u7684\u6548\u679c\u5bf9 \u7ec4\u5b66\u6570\u636e\u77e9\u9635\u7684\u5f71\u54cd\u3002ARSyN\u53ef\u4ee5\u53bb\u9664\u4e0d\u9700\u8981\u7684\u4fe1\u53f7\uff0c\u4ece\u800c\u83b7\u5f97\u7ecf\u8fc7\u566a\u58f0\u8fc7\u6ee4\u7684\u6570\u636e\uff0c\u4ee5\u4fbf\u8fdb\u884c\u8fdb\u4e00\u6b65\u7684\u5206\u6790\uff08<\/span>1<\/span>\uff09\u3002\u5728<\/span>MultiBaC<\/span>\u5305\u4e2d\uff0cARSyN\u88ab\u7528\u4e8e\u8fc7\u6ee4\u4e0e\u5df2\u8bc6\u522b\u6216\u672a\u8bc6\u522b\u7684\u6279\u6b21\u6548\u5e94\u76f8\u5173\u7684\u566a\u58f0\u3002\u8fd9\u79cd\u9002\u5e94\u6027\u88ab\u79f0\u4e3aARSyNbac\u3002 \u5728ARSyN\u65b9\u6cd5\u4e2d\uff0cANOVA\u6a21\u578b\u5c06\u6bcf\u4e2a\u56e0\u7d20\u5728\u5b9e\u9a8c\u8bbe\u8ba1\u4e2d\u8bc6\u522b\u7684\u4fe1\u53f7\u4e0e\u6b8b\u5dee\u5206\u5f00\u3002\u8be5\u7b97\u6cd5\u53ef\u5e94\u7528\u4e8e\u591a\u56e0\u7d20\u5b9e\u9a8c\u8bbe\u8ba1\u3002\u5982\u679c\u5df2\u77e5\u6bcf\u4e2a\u6837\u672c\u6240\u5c5e\u7684\u6279\u6b21\u4fe1\u606f\uff0c\u5219\u6a21\u578b\u4e2d\u7684\u4e00\u4e2a\u56e0\u7d20\u53ef\u4ee5\u662f\u6279\u6b21\u3002\u5728\u8fd9\u79cd\u60c5\u51b5\u4e0b\uff0cANOVA\u6a21\u578b\u5c06\u7528\u4e8e\u5c06\u6279\u6b21\u6548\u5e94\u4e0e\u5176\u4ed6\u6548\u5e94\u548c\u6b8b\u5dee\u5206\u5f00\u3002\u56e0\u6b64\uff0cPCA\u5206\u6790\u5c06\u68c0\u6d4b\u5230\u7531\u4e8e\u6279\u6b21\u6548\u5e94\u800c\u53ef\u80fd\u5b58\u5728\u7684\u7ed3\u6784\u5316\u53d8\u5f02\uff0c\u5373\u7531\u89e3\u91ca\u6570\u636e\u603b\u53d8\u5f02\u4e2d\u7ed9\u5b9a\u6bd4\u4f8b\u7684\u4e3b\u6210\u5206\u8bc6\u522b\u7684\u53d8\u5f02\uff0c\u7528\u6237\u53ef\u4ee5\u8bbe\u7f6e\u8be5\u6bd4\u4f8b\u3002 \u6b64\u5916\uff0c\u5f53\u672a\u77e5\u6279\u6b21\u56e0\u5b50\u65f6\uff0c\u4e5f\u53ef\u4ee5\u5e94\u7528ARSyN\uff0c\u56e0\u4e3a\u5bf9\u6b8b\u5dee\u77e9\u9635\u8fdb\u884cPCA\u53ef\u4ee5\u68c0\u6d4b\u5230\u4e0e\u5b9e\u9a8c\u8bbe\u8ba1\u4e2d\u672a\u5305\u62ec\u7684\u53d8\u5f02\u6e90\u76f8\u5173\u7684\u5173\u8054\u7ed3\u6784\u3002\u5f53PCA\u7684\u7b2c\u4e00\u7279\u5f81\u503c\u660e\u663e\u9ad8\u4e8e\u5176\u4ed6\u7279\u5f81\u503c\u65f6\uff0c\u6211\u4eec\u4f1a\u6ce8\u610f\u5230\u6b8b\u5dee\u4e2d\u7684\u8fd9\u79cd\u4fe1\u53f7\uff0c\u56e0\u4e3a\u5982\u679c\u6ca1\u6709\u4efb\u4f55\u7ed3\u6784\uff0c\u7279\u5f81\u503c\u5927\u81f4\u76f8\u7b49\u3002\u5728\u8fd9\u79cd\u60c5\u51b5\u4e0b\uff0c\u7ec4\u4ef6\u7684\u9009\u62e9\u7531\u03b2\u53c2\u6570\u63a7\u5236\u3002\u8868\u793a\u7cfb\u7edf\u6027\u566a\u58f0\u5e76\u4ece\u539f\u59cb\u6570\u636e\u4e2d\u5220\u9664\u7684\u7ec4\u4ef6\u662f\u90a3\u4e9b\u4ee3\u8868\u5e73\u5747\u53d8\u5f02\u6027\u8d85\u8fc7\u03b2\u500d\u7684\u7ec4\u4ef6\u3002<\/span><\/span><\/p>\n<section style=\"font-size: 16px;margin-bottom: 0px;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(69, 107, 176);padding-right: 6px;padding-bottom: 6px;padding-left: 6px;\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;transform: translate3d(19px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"text-align: justify;color: rgb(255, 255, 255);\">\n <\/p>\n<\/section>\n<\/section>\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;background-color: rgb(255, 255, 255);padding: 23px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n\u516c\u4f17\u53f7\u540e\u53f0\u56de\u590d\u201c111\u201d<\/span>\u9886\u53d6\u672c\u7bc7\u4ee3\u7801\u3001\u57fa\u56e0\u96c6\u6216\u793a\u4f8b\u6570\u636e\u7b49\u6587\u4ef6\uff1b<\/p>\n\u6587\u4ef6\u7f16\u53f7\uff1a231210<\/strong><\/em><\/span><\/p>\n\u679c\u7c89\u798f\u5229<\/span><\/strong>\uff1a\u751f\u4fe1\u4eba\u5fc5\u5907\u795e\u5668\u2014\u2014\u670d\u52a1\u5668<\/strong><\/span> <\/p>\n\u5e73\u65f6\u751f\u4fe1\u5206\u6790\u5b66\u4e60\u4e2d\u6709\u8981\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u8054\u7cfb\u5c0f\u679c\u79df\u8d41\uff0c\u7c89\u4e1d\u798f\u5229\u90fd\u662f\u5e02\u573a\u8d85\u4f4e\u4ef7\u683c\uff0c\u8d76\u5feb\u627e\u5c0f\u679c\u9886\u53d6\u514d\u8d39\u7684\u8bd5\u7528\u8d26\u53f7\u5427\uff01<\/p>\n<a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247495825&idx=2&sn=a22a72496a1c082ea5b827be94ce4d99&chksm=cf7f6054f808e94264e14bfed4359cab3fcaaca249952a9f761c37ece352dcd7108579788b89&scene=21#wechat_redirect\" textvalue=\"\u670d\u52a1\u5668\u4ef7\u683c\u914d\u7f6e\u8868\uff08\u70b9\u51fb\u94fe\u63a5\u67e5\u770b\uff09\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" rel=\"noopener\">\u670d\u52a1\u5668\u4ef7\u683c\u914d\u7f6e\u8868\uff08\u70b9\u51fb\u94fe\u63a5\u67e5\u770b\uff09<\/a><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n\u793a\u4f8b\uff1a\u9175\u6bcd\u8868\u8fbe\u6570\u636e<\/strong><\/span><\/p>\n\u9175\u6bcd\u8868\u8fbe\u4f8b\u6570\u636e\u96c6\u4eceGene Expression Omnibus\uff08GEO\uff09\u6570\u636e\u5e93\u548c\u4e09\u4e2a\u4e0d\u540c\u7684\u5b9e\u9a8c\u5ba4\uff08\u6279\u6b21\uff09\u4e2d\u6536\u96c6\u3002\u5728\u6240\u6709\u8fd9\u4e9b\u6570\u636e\u96c6\u4e2d\uff0c\u5206\u6790\u4e86\u9175\u6bcd\u4e2d\u8461\u8404\u7cd6\u9965\u997f\u7684\u5f71\u54cd\u3002Lab A\u662fUniversitat de Valencia\u7684\u751f\u7269\u5316\u5b66\u548c\u5206\u5b50\u751f\u7269\u5b66\u90e8\u95e8\uff08\u5b58\u53d6\u53f7GSE11521\uff09[<\/span>2<\/span>]; Lab B\u662f\u54c8\u4f5b\u5927\u5b66\u7684\u5206\u5b50\u548c\u7ec6\u80de\u751f\u7269\u5b66\u90e8\u95e8\uff08\u5b58\u53d6\u53f7GSE56622\uff09[<\/span>5<\/span>]; \u548cLab C\u662f\u7ea6\u7ff0\u970d\u666e\u91d1\u65af\u5927\u5b66\u7684\u751f\u7269\u5b66\u90e8\u95e8\uff08\u5b58\u53d6\u53f7GSE43747\uff09[<\/span>6<\/span>]\u3002 \u5bf9\u4e8e\u6bcf\u4e2a\u75c5\u4f8b\u8fdb\u884c\u9002\u5f53\u7684\u6570\u636e\u9884\u5904\u7406\u540e\uff0c\u5fc5\u8981\u65f6\u5e94\u7528\u4e86voom\u8f6c\u6362\uff08\u4f7f\u7528limma R\u5305\uff09\u3002\u6700\u540e\uff0c\u5bf9\u6765\u81ea\u6240\u6709\u5b9e\u9a8c\u5ba4\u7684\u6240\u6709\u6837\u672c\u8fdb\u884c\u4e86TMM\u5f52\u4e00\u5316\u3002\u901a\u8fc7\u4ece\u6bcf\u4e2a\u6570\u636e\u77e9\u9635\u4e2d\u9009\u62e9200\u4e2a\u7ec4\u5b66\u53d8\u91cf\u5e76\u4ec5\u4eceA\u5b9e\u9a8c\u5ba4\u9009\u62e93\u4e2a\u6837\u672c\uff0c\u83b7\u5f97\u4e86\u51cf\u5c11\u7684\u6570\u636e\u96c6\u3002\u8fd9\u4e2a\u9175\u6bcd\u591a\u7ec4\u5b66\u51cf\u5c11\u7684\u6570\u636e\u96c6\u5305\u542b\u5728<\/span>MutiBaC<\/span>\u5305\u4e2d\uff0c\u7528\u4e8e\u8bf4\u660e\u8be5\u5305\u7684\u7528\u6cd5\u3002\u53ef\u4ee5\u4f7f\u7528<\/span>data(\u201cmultiyeast\u201d\uff09<\/span>\u6307\u4ee4\u52a0\u8f7d\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u3002 \u8fd9\u4e09\u9879\u7814\u7a76\u4f7f\u7528\u4e86\u76f8\u5f53\u7684\u9175\u6bcd\u83cc\u682a\u548c\u5b9e\u9a8c\u6761\u4ef6\uff0c\u4f46\u5982\u56fe1\u6240\u793a\uff0c\u5bf9\u8868\u8fbe\u7684\u4e3b\u8981\u5f71\u54cd\u662f\u7531\u4e8e\u5c5e\u4e8e\u4e0d\u540c\u5b9e\u9a8c\u5ba4\u7684\u6570\u636e\uff0c\u5373\u672c\u4f8b\u4e2d\u7684\u6279\u6b21\u3002 <img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014465\" data-ratio=\"0.5601851851851852\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_H9IkhYjUsxTsbjnCCdrqX5h4AB4eMQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSvXrLibRUlbBT315KFd6wibzBhqH9IkhYjUsxTsbjnCCdrqX5h4AB4eMQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"313.6000061035156\" width=\"560.010009765625\" \/> <\/span><\/span>\u56fe1\uff1a<\/span>\u539f\u59cb\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684\u4e3b\u6210\u5206\u5206\u6790\u56fe\uff08\u6821\u6b63\u524d\uff09<\/span>\u6279\u6b21\u4e4b\u95f4\u5b8c\u5168\u5206\u5f00\u3002\u4f7f\u7528MultiBaC\u5305\u751f\u6210\u7684\u56fe\uff08\u89c1\u7ed3\u679c\u53ef\u89c6\u5316\u90e8\u5206)\u3002<\/span> <\/span> <\/span><o:page><\/o:page><\/p>\nARSyNbac\u8f93\u5165\u6570\u636e<\/strong><\/span><\/p>\nMultiBaC<\/span>\u5305\u4f7f\u7528\u7684\u662f<\/span>MultiAssayExperiment<\/span>\u5bf9\u8c61\uff0c\u8fd9\u662fBioconductor\u4e3a\u591a\u7ec4\u5b66\u7814\u7a76\u63d0\u4f9b\u7684\u4e00\u79cd\u5bb9\u5668\u7c7b\u578b\uff0c\u53ef\u4ee5\u4ece\u4e00\u4e2a\u7531\u77e9\u9635\u6216<\/span>data.frame<\/span>\u5bf9\u8c61\u7ec4\u6210\u7684\u5217\u8868\u4e2d\u521b\u5efa\u51fa\u6765\u3002\u8fd9\u4e9b\u77e9\u9635\u5fc5\u987b\u5177\u6709\u4ee5\u884c\u4e3a\u7279\u5f81\u3001\u4ee5\u5217\u4e3a\u6837\u54c1\u7684\u5e03\u5c40\uff0c\u5982\u4e0b\u9762\u6240\u793a\u7684\u9175\u6bcd\u793a\u4f8b\u6570\u636e\u77e9\u9635\u4e4b\u4e00(A.rna)\u3002\u91cd\u8981\u7684\u662f\uff0c\u6240\u6709\u6570\u636e\u77e9\u9635\u90fd\u5e94\u5177\u6709\u76f8\u540c\u7684\u53d8\u91cf\u7a7a\u95f4\u3002\u5982\u679c\u5404\u7ec4\u5b66\u7684\u53d8\u91cf\u6570\u91cf\u548c\u987a\u5e8f\u4e0d\u4e00\u81f4\uff0c\u90a3\u4e48<\/span>createMbac<\/span>\u51fd\u6570\u5c06\u4f1a\u9009\u62e9\u5171\u6709\u7684\u53d8\u91cf\u3002\u56e0\u6b64\uff0c\u6240\u6709\u884c\u5fc5\u987b\u4f7f\u7528\u540c\u7c7b\u578b\u7684\u6807\u8bc6\u7b26\u8fdb\u884c\u547d\u540d\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"css\"><code>data<\/span>(\"multiyeast<\/span>\") <\/span><\/code><code>head<\/span>(A<\/span>.rna<\/span>) <\/span><\/code><code>## A<\/span>.rna_Glu<\/span>+_1 A<\/span>.rna_Glu<\/span>+_2 A<\/span>.rna_Glu<\/span>+_3 A<\/span>.rna_Glu-_1<\/span> A<\/span>.rna_Glu-_2<\/span> <\/span><\/code><code>## YOR324C<\/span> 7.174264<\/span> 6.976815<\/span> 7.482661<\/span> 8.020596<\/span> 7.736636<\/span> <\/span><\/code><code>## YGL104C<\/span> 4.239493<\/span> 4.284775<\/span> 3.100898<\/span> 4.957403<\/span> 3.673252<\/span> <\/span><\/code><code>## YOR142W<\/span> 8.819824<\/span> 8.496966<\/span> 9.026971<\/span> 10.374525<\/span> 10.294006<\/span> <\/span><\/code><code>## YOR052C<\/span> 6.721211<\/span> 7.011932<\/span> 7.557519<\/span> 8.504503<\/span> 8.586738<\/span> <\/span><\/code><code>## YGR038W<\/span> 5.878483<\/span> 5.894121<\/span> 6.468361<\/span> 7.856822<\/span> 7.806318<\/span> <\/span><\/code><code>## YER087W<\/span> 5.131089<\/span> 5.295029<\/span> 5.750657<\/span> 2.920250<\/span> 5.496136<\/span> <\/span><\/code><code>## A<\/span>.rna_Glu-_3<\/span> <\/span><\/code><code>## YOR324C<\/span> 7.922425<\/span> <\/span><\/code><code>## YGL104C<\/span> 1.587184<\/span> <\/span><\/code><code>## YOR142W<\/span> 10.979224<\/span> <\/span><\/code><code>## YOR052C<\/span> 8.221168<\/span> <\/span><\/code><code>## YGR038W<\/span> 8.108436<\/span> <\/span><\/code><code>## YER087W<\/span> 2.879254<\/span><\/span><\/code><\/pre>\n<\/section>\n\u5bf9\u4e8e\u6bcf\u4e2a\u6279\u6b21\uff08\u672c\u4f8b\u4e2d\u7684\u5b9e\u9a8c\u5ba4\uff09\uff0c\u9700\u8981\u521b\u5efa\u4e00\u4e2a\u201cMultiAssayExperiment\u201d\u5bf9\u8c61\u3002\u65b0\u7684\u6570\u636e\u7ed3\u6784\u201cmbac\u201d\u662f\u4e00\u4e2a\u201cMultiAssayExperiment\u201d\u5bf9\u8c61\u7684\u5217\u8868\uff0c\u53ef\u4ee5\u4f7f\u7528\u5305\u4e2d\u7684\u201ccreateMbac\u201d\u51fd\u6570\u8f7b\u677e\u751f\u6210\u3002\u751f\u6210\u7684\u201cmbac\u201d\u5bf9\u8c61\u5c06\u662f\u201cARSyNbac\u201d\u7684\u8f93\u5165\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"swift\"><code>data_RNA<-createMbac (inputOmics =list(A<\/span>.rna, B<\/span>.rna, C<\/span>.rna), <\/span><\/code><code> batchFactor =c<\/span>(\"A\"<\/span>, \"B\"<\/span>, \"C\"<\/span>), <\/span><\/code><code> experimentalDesign =list(\"A\"<\/span>= c<\/span>(\"Glu+\"<\/span>, \"Glu+\"<\/span>, <\/span><\/code><code> \"Glu+\"<\/span>, \"Glu-\"<\/span>, <\/span><\/code><code> \"Glu-\"<\/span>, \"Glu-\"<\/span>), <\/span><\/code><code> \"B\"<\/span>=c<\/span>(\"Glu+\"<\/span>, \"Glu+\"<\/span>, <\/span><\/code><code> \"Glu-\"<\/span>, \"Glu-\"<\/span>), <\/span><\/code><code> \"C\"<\/span>=c<\/span>(\"Glu+\"<\/span>, \"Glu+\"<\/span>, <\/span><\/code><code> \"Glu-\"<\/span>, \"Glu-\"<\/span>)), <\/span><\/code><code> omicNames =\"RNA\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n\u4ee5\u4e0b\u662f<\/span>createMbac<\/span>\u51fd\u6570\u53c2\u6570\u7684\u8bf4\u660e\uff1a<\/span><\/span><\/p>\n\u2022<\/span>inputOmics<\/span> \u5305\u542b\u8981\u5206\u6790\u7684\u6240\u6709\u77e9\u9635\u6216\u6570\u636e\u6846\u5bf9\u8c61\u7684\u5217\u8868\u3002\u4e5f\u53ef\u4ee5\u63d0\u4f9b MultiAssayExperiment \u5bf9\u8c61\u3002<\/span><\/span><\/p>\n\u2022<\/span>batchFactor<\/span> \u4e00\u4e2a\u5411\u91cf\u6216\u56e0\u5b50\uff0c\u6307\u793a\u6bcf\u4e2a\u8f93\u5165\u77e9\u9635\u6240\u5c5e\u7684\u6279\u6b21\uff08\u5373\u7814\u7a76\u3001\u5b9e\u9a8c\u5ba4\u3001\u65f6\u95f4\u70b9\u7b49\uff09\u3002\u5982\u679c\u4e3a NULL\uff08\u9ed8\u8ba4\u503c\uff09\uff0c\u5219\u4e0d\u8003\u8651\u6279\u6b21\uff0c\u53ea\u53ef\u4f7f\u7528 ARSyNbac \u566a\u58f0\u51cf\u5c11\u6a21\u5f0f\u3002<\/span><\/span><\/p>\n\u2022<\/span>experimentalDesign<\/span> \u5305\u542b\u4e0e\u6279\u6b21\u6570\u91cf\u76f8\u540c\u7684\u5143\u7d20\u7684\u5217\u8868\u3002\u6bcf\u4e2a\u5143\u7d20\u53ef\u4ee5\u662f\u56e0\u5b50\u3001\u5b57\u7b26\u5411\u91cf\u6216\u6570\u636e\u6846\uff0c\u8868\u793a\u8be5\u6279\u6b21\u4e2d\u6bcf\u4e2a\u6837\u672c\u7684\u5b9e\u9a8c\u6761\u4ef6\u3002\u5f53\u662f\u5177\u6709\u591a\u5217\uff08\u591a\u56e0\u7d20\u5b9e\u9a8c\u8bbe\u8ba1\uff09\u7684\u6570\u636e\u6846\u65f6\uff0c\u4e0d\u540c\u5217\u5c06\u7ec4\u5408\u6210\u4e00\u4e2a\u5355\u4e00\u5217\uff0c\u7531 MultiBaC \u6216 ARSyNbac \u4f7f\u7528\u3002\u5728\u4efb\u4f55\u60c5\u51b5\u4e0b\uff0c\u5b9e\u9a8c\u8bbe\u7f6e\u5fc5\u987b\u5bf9\u6240\u6709\u6279\u6b21\u76f8\u540c\u3002\u6b64\u5916\uff0c\u6b64\u5217\u8868\u4e2d\u5143\u7d20\u7684\u540d\u5b57\u5fc5\u987b\u4e0e <\/span>batches<\/span> \u53c2\u6570\u4e2d\u58f0\u660e\u7684\u540d\u5b57\u76f8\u540c\u3002\u5982\u679c\u4e0d\u76f8\u540c\uff08\u6216\u4e3a NULL\uff09\uff0c\u5219\u5f3a\u5236\u5c06\u540d\u79f0\u4e0e <\/span>batches<\/span> \u53c2\u6570\u4e2d\u7684\u540d\u79f0\u76f8\u540c\u5e76\u6309\u76f8\u540c\u987a\u5e8f\u6392\u5217\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n\u2022<\/span>omicNames<\/span> \u6bcf\u4e2a\u8f93\u5165\u77e9\u9635\u7684\u540d\u79f0\u5411\u91cf\u3002\u8981\u6c42\u5171\u6709\u7684 omic \u5728\u6240\u6709\u6279\u6b21\u4e2d\u5177\u6709\u76f8\u540c\u7684\u540d\u79f0\u3002<\/span><\/span><\/p>\n\u2022<\/span>commonOmic<\/span> \u6279\u6b21\u4e4b\u95f4\u5171\u6709\u7684 omic \u7684\u540d\u79f0\u3002\u5fc5\u987b\u662f omicNames \u53c2\u6570\u4e2d\u7684\u4e00\u4e2a\u540d\u79f0\u3002\u5982\u679c\u4e3a NULL\uff08\u9ed8\u8ba4\u503c\uff09\uff0c\u5c06\u9009\u62e9\u6240\u6709\u6279\u6b21\u4e2d\u5171\u6709\u7684 omic \u540d\u79f0\u4f5c\u4e3a commonOmic\u3002 \u7531createMbac\u51fd\u6570\u751f\u6210\u7684mbac R\u7ed3\u6784\u662f\u4e00\u4e2aS3\u5bf9\u8c61\uff0c\u6700\u521d\u53ea\u5305\u542b\u4e00\u4e2a\u69fd\uff0c\u5373ListOfBatches\u5bf9\u8c61\u3002\u5f53\u8fd0\u884cARSyNbac\u6216MultiBaC\u51fd\u6570\u65f6\uff0c\u968f\u7740\u5b83\u4eec\u88ab\u521b\u5efa\uff0c\u8fd9\u4e2ambac\u7ed3\u6784\u5c06\u5305\u542b\u66f4\u591a\u7684\u5143\u7d20\u3002\u8fd9\u4e9b\u65b0\u69fd\u662fCorrectedData\u3001PLSmodels\u3001ARSyNmodels\u6216InnerRelation\uff0c\u4e0b\u9762\u8fdb\u884c\u63cf\u8ff0\uff1a<\/span><\/span><\/p>\n\u2022<\/span>ListOfBatches<\/span>: \u4e00\u4e2a\u5305\u542b\u591a\u4e2aMultiAssayExperiment\u5bf9\u8c61\u7684\u5217\u8868\uff08\u6bcf\u4e2a\u6279\u6b21\u4e00\u4e2a\u5bf9\u8c61\uff09\u3002<\/span><\/span><\/p>\n\u2022<\/span>CorrectedData<\/span>: \u4e0eListOfBatches\u7ed3\u6784\u76f8\u540c\uff0c\u4f46\u662f\u5305\u542b\u4fee\u6b63\u540e\u7684\u6570\u636e\u77e9\u9635\uff0c\u800c\u4e0d\u662f\u539f\u59cb\u77e9\u9635\u3002<\/span><\/span><\/p>\n\u2022<\/span>PLSmodels<\/span>: \u7531MultiBaC\u65b9\u6cd5\u521b\u5efa\u7684PLS\u6a21\u578b\uff08\u6bcf\u4e2a\u975e\u516c\u5171omic\u6570\u636e\u7c7b\u578b\u4e00\u4e2a\u6a21\u578b\uff09\u3002\u4ec5\u9002\u7528\u4e8eMultiBaC\u65b9\u6cd5\u3002<\/span><\/span><\/p>\n\u2022<\/span>ARSyNmodels<\/span>: \u7531ARSyNbac\u6216MultiBaC\u51fd\u6570\u521b\u5efa\u7684ARSyN\u6a21\u578b\u3002<\/span><\/span><\/p>\n\u2022<\/span>InnerRelation<\/span>: \u4e00\u4e2a\u7c7b\u4e3a<\/span>data.frame<\/span>\u7684\u8868\uff0c\u5305\u542b\u6bcf\u4e2aPLS\u6a21\u578b\u5728\u6240\u6709\u7ec4\u4ef6\u95f4\u7684\u5185\u90e8\u76f8\u5173\u6027\uff08\u5373X\uff08t\uff09\u548cY\uff08u\uff09\u77e9\u9635\u5f97\u5206\u95f4\u7684\u76f8\u5173\u6027\uff09\uff0c\u7528\u4e8e\u6a21\u578b\u9a8c\u8bc1\u3002\u4ec5\u9002\u7528\u4e8eMultiBaC\u65b9\u6cd5\u3002<\/span><\/span><\/p>\n\u2022<\/span>commonOmic<\/span>: \u6279\u6b21\u95f4\u516c\u5171omic\u7684\u540d\u79f0\u3002 \u9664\u4e86\u7ed8\u56fe\u4e4b\u5916\uff0c\u8fd8\u63d0\u4f9b\u4e86\u7528\u4e8e\u53ef\u89c6\u5316mbac\u5bf9\u8c61\u7684\u5176\u4ed6\u65b9\u6cd5\uff1a\u6458\u8981\uff0c\u5b83\u663e\u793a\u4e86\u5bf9\u8c61\u7684\u7ed3\u6784\u3002<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code>summary(data_RNA) <\/span><\/code><code>#<\/span># [1] \"Object of class mbac: It contains 3 different bacthes and 1 omic type(s).\"<\/span><\/span><\/code><\/pre>\n<\/section>\n<table border=\"1\" cellspacing=\"0\" cellpadding=\"0\" style=\"margin-left: 0px;border-width: initial;border-style: none;border-color: initial;border-collapse: collapse;width: 100%;\">\n<thead>\n<tr>\n<td width=\"264\" valign=\"top\" style=\"border-width: initial;border-style: none;border-color: initial;padding: 0pt 5.4pt;word-break: break-all;\">\n <o:p> <\/o:p><\/span><\/p>\n<\/td>\n<td width=\"264\" valign=\"top\" style=\"border-top:none;border-left:none;border-bottom:none;border-right:none;padding:0pt 5.4pt 0pt 5.4pt;\">\nRNA<\/span><\/p>\n<\/td>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td width=\"264\" valign=\"top\" style=\"border-top:none;border-left:none;border-bottom:none;border-right:none;padding:0pt 5.4pt 0pt 5.4pt;\">\nA<\/span><\/p>\n<\/td>\n<td width=\"264\" valign=\"top\" style=\"border-top:none;border-left:none;border-bottom:none;border-right:none;padding:0pt 5.4pt 0pt 5.4pt;\">\nTrue<\/span><\/p>\n<\/td>\n<\/tr>\n<tr>\n<td width=\"264\" valign=\"top\" style=\"border-top:none;border-left:none;border-bottom:none;border-right:none;padding:0pt 5.4pt 0pt 5.4pt;\">\nB<\/span> <\/span><o:page><\/o:page><\/p>\n<\/td>\n<td width=\"264\" valign=\"top\" style=\"border-top:none;border-left:none;border-bottom:none;border-right:none;padding:0pt 5.4pt 0pt 5.4pt;\">\nTrue<\/span><\/p>\n<\/td>\n<\/tr>\n<tr>\n<td width=\"264\" valign=\"top\" style=\"border-top:none;border-left:none;border-bottom:none;border-right:none;padding:0pt 5.4pt 0pt 5.4pt;\">\nC<\/span><\/p>\n<\/td>\n<td width=\"264\" valign=\"top\" style=\"border-top:none;border-left:none;border-bottom:none;border-right:none;padding:0pt 5.4pt 0pt 5.4pt;\">\nTrue<\/span><\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100014488\" data-ratio=\"0.38981481481481484\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_IWicymEetCc6Enf2BkUE4Yz1Ya5e5w-2.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyuYsqlJnQUJvnS2iciaDibtfbdV0VmHlriaSjYwjFPLp1BLjokHIWicymEetCc6Enf2BkUE4Yz1Ya5e5w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"letter-spacing: 0.578px;text-wrap: wrap;color: rgb(34, 34, 38);font-family: "Times New Roman";font-size: 15px;font-weight: 700;background-color: rgb(255, 255, 255);text-align: center;\" \/>ARSyNbac\u6821\u6b63<\/strong><\/span><\/p>\nMultiBaC<\/span>\u5305\u4e2d\u7528\u4e8e\u4ece\u5355\u4e00\u6837\u672c\u6570\u636e\u77e9\u9635\u4e2d\u53bb\u9664\u6279\u6b21\u6548\u5e94\u6216\u4e0d\u9700\u8981\u7684\u566a\u58f0\u7684\u51fd\u6570\u662f<\/span>ARSyNbac<\/span>\u51fd\u6570\uff0c\u5b83\u5141\u8bb8\u4ee5\u4e0b\u53c2\u6570\uff1a<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code>ARSyNbac (mbac, batchEstimation = TRUE<\/span>, filterNoise = TRUE<\/span>, <\/span><\/code><code> Interaction=FALSE<\/span>, Variability = 0.90<\/span>, beta = 2<\/span>, <\/span><\/code><code> modelName = \"Model 1\"<\/span>, <\/span><\/code><code> showplot = TRUE<\/span>)<\/span><\/code><\/pre>\n<\/section>\n\u2022<\/span>mbac<\/span>: \u901a\u8fc7 <\/span>createMbac<\/span> \u751f\u6210\u7684 mbac \u5bf9\u8c61\u3002<\/span><\/span><\/p>\n\u2022<\/span>batchEstimation<\/span>: \u903b\u8f91\u503c\u3002\u5982\u679c\u4e3a TRUE\uff08\u9ed8\u8ba4\u503c\uff09\uff0c\u5219\u4f30\u7b97\u6279\u6b21\u6548\u5e94\u5e76\u7528\u4e8e\u6821\u6b63\u6570\u636e\u3002\u5f53\u5df2\u77e5\u6279\u6b21\u6548\u5e94\u7684\u6765\u6e90\u65f6\uff0c\u8bf7\u4f7f\u7528 TRUE\u3002<\/span><\/span><\/p>\n\u2022<\/span>filterNoise<\/span>: \u903b\u8f91\u503c\u3002\u5982\u679c\u4e3a TRUE\uff08\u9ed8\u8ba4\u503c\uff09\uff0c\u5219\u4ece\u6b8b\u5dee\u4e2d\u79fb\u9664\u7ed3\u6784\u5316\u566a\u58f0\u3002\u5f53\u6570\u636e\u4e2d\u5b58\u5728\u672a\u77e5\u6279\u6b21\u6548\u5e94\u6765\u6e90\u65f6\uff0c\u8bf7\u4f7f\u7528\u6b64\u9009\u9879\u3002<\/span><\/span><\/p>\n\u2022<\/span>Interaction<\/span>: \u903b\u8f91\u503c\u3002\u662f\u5426\u5efa\u7acb\u56e0\u7d20\u4e4b\u95f4\u7684\u4ea4\u4e92\u6a21\u578b\uff08\u9ed8\u8ba4\u4e3a FALSE\uff09\u3002<\/span><\/span><\/p>\n\u2022<\/span>Variability<\/span>: \u4ece 0 \u5230 1 \u7684\u503c\u3002\u6bcf\u4e2a\u6a21\u578b\u5fc5\u987b\u89e3\u91ca\u7684\u6570\u636e\u53d8\u5f02\u6027\u7684\u6700\u5c0f\u767e\u5206\u6bd4\u3002\u5728\u6279\u6b21\u6821\u6b63\u6a21\u5f0f\u4e0b\u4f7f\u7528\u3002\u9ed8\u8ba4\u503c\u4e3a 0.90\u3002<\/span><\/span><\/p>\n\u2022<\/span>beta<\/span>: \u6570\u503c\u3002\u8868\u793a\u8d85\u8fc7\u5e73\u5747\u53d8\u5f02\u6027\u7684 beta \u500d\u7684\u7ec4\u4ef6\u88ab\u786e\u5b9a\u4e3a\u6b8b\u5dee\u4e2d\u7684\u7cfb\u7edf\u566a\u58f0\u3002\u5728\u566a\u58f0\u51cf\u5c11\u6a21\u5f0f\u4e0b\u4f7f\u7528\u3002\u9ed8\u8ba4\u503c\u4e3a 2\u3002<\/span><\/span><\/p>\n\u2022<\/span>modelName<\/span>: \u521b\u5efa\u7684\u6a21\u578b\u7684\u540d\u79f0\u3002\u5982\u679c\u60a8\u4f7f\u7528 explaine_var \u7ed8\u56fe\u51fd\u6570\uff0c\u5219\u4f1a\u663e\u793a\u6b64\u540d\u79f0\u3002\u9ed8\u8ba4\u503c\u4e3a \u201cModel 1\u201d\u3002<\/span><\/span><\/p>\n\u2022<\/span>showplot<\/span>: \u903b\u8f91\u503c\u3002\u5982\u679c\u4e3a TRUE\uff08\u9ed8\u8ba4\u503c\uff09\uff0c\u5219\u663e\u793a explained_var \u7ed8\u56fe\u3002\u6b64\u7ed8\u56fe\u8868\u793a ARSyN \u6a21\u578b\u9009\u62e9\u7684\u7ec4\u4ef6\u6570\u91cf\u3002 \u56e0\u6b64\uff0c<\/span>ARSyNbac\u51fd\u6570\u63d0\u4f9b\u4e86\u4e09\u79cd\u5206\u6790\u7c7b\u578b\uff1a\u5f53\u63d0\u4f9b\u6279\u6b21\u4fe1\u606f\u65f6\u8fdb\u884c<\/span>ARSyNbac\u6279\u6b21\u6548\u5e94\u6821\u6b63<\/span>\uff0c\u5f53\u6279\u6b21\u4fe1\u606f\u672a\u77e5\u65f6\u8fdb\u884c<\/span>ARSyNbac\u566a\u58f0\u6291\u5236<\/span>\uff0c\u5f53\u5b58\u5728\u5df2\u77e5\u6279\u6b21\u6548\u5e94\u6e90\u548c\u53e6\u4e00\u4e2a\u53ef\u80fd\u7684\u672a\u77e5\u4e0d\u9700\u8981\u7684\u53ef\u53d8\u6027\u6e90\u65f6\u8fdb\u884c\u4e24\u8005\u7684\u7ec4\u5408\u6a21\u5f0f\u3002\u4ee5\u4e0b\u90e8\u5206\u8bf4\u660e\u5982\u4f55\u8fdb\u884c\u6bcf\u4e00\u79cd\u5206\u6790\u3002<\/span> <\/span><o:page><\/o:page><\/p>\nARSyNbac\u6279\u91cf\u6548\u5e94\u6821\u6b63<\/strong><\/span><\/p>\n\u5f53\u5728<\/span>mbac<\/span>\u8f93\u5165\u5bf9\u8c61\u7684<\/span>batchFactor<\/span>\u53c2\u6570\u4e2d\u6307\u5b9a\u6279\u6b21\u65f6\uff0c\u53ef\u4ee5\u901a\u8fc7\u9009\u62e9<\/span>batchEstimation = TRUE<\/span>\uff08\u4ec5\u8003\u8651\u4e00\u4e2a\u6279\u6b21\u6548\u5e94\u6e90\uff0c<\/span>filterNoise = FALSE<\/span>\uff09\u6765\u4f30\u8ba1\u5e76\u6d88\u9664\u5176\u5f71\u54cd\u3002\u6b64\u5916\uff0c\u901a\u8fc7\u8bbe\u7f6e<\/span>Interaction=TRUE<\/span>\u53ef\u4ee5\u7814\u7a76\u5b9e\u9a8c\u56e0\u7d20\u4e0e\u6279\u6b21\u56e0\u7d20\u4e4b\u95f4\u7684\u76f8\u4e92\u4f5c\u7528\u3002<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code>par(mfrow = c(1<\/span>,2<\/span>)) <\/span><\/code><code>arsyn_1 <- ARSyNbac(data_RNA, modelName = \"RNA\"<\/span>, Variability = 0.95<\/span>, <\/span><\/code><code> batchEstimation = TRUE<\/span>, filterNoise = FALSE<\/span>, Interaction = FALSE<\/span>) <\/span><\/code><code>plot(arsyn_1, typeP=\"pca.cor\"<\/span>, bty = \"L\"<\/span>, <\/span><\/code><code> pch = custom_pch, cex = 3<\/span>, col.per.group = custom_col, <\/span><\/code><code> legend.text = c(\"Color: Batch\"<\/span>, names(data_RNA$ListOfBatches), <\/span><\/code><code> \"Fill: Cond.\"<\/span>, unique(colData(data_RNA$ListOfBatches$A)$tfactor)), <\/span><\/code><code> args.legend = list<\/span>(\"x\"<\/span> = \"topright\"<\/span>, <\/span><\/code><code> \"pch\"<\/span> = c(NA, 15<\/span>, 15<\/span>, 15<\/span>, <\/span><\/code><code> NA, 15<\/span>, 0<\/span>), <\/span><\/code><code> \"col\"<\/span> = c(NA, \"brown2\"<\/span>, \"dodgerblue\"<\/span>, \"forestgreen\"<\/span>, <\/span><\/code><code> NA, 1<\/span>, 1<\/span>), <\/span><\/code><code> \"bty\"<\/span> = \"n\"<\/span>, <\/span><\/code><code> \"cex\"<\/span> = 1.2<\/span>))<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014467\" data-ratio=\"0.5574074074074075\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_gvuSTbB5M5OVH38Dnvj2z4DE4iaE6g.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSc1nbCcYcp9E6zuovWsWBKLTxqgvuSTbB5M5OVH38Dnvj2z4DE4iaE6g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"312.0\" width=\"560.010009765625\" \/><\/span> <\/span>\u56fe2\uff1a<\/span>\u4e0d\u8003\u8651\u4ea4\u4e92\u4f5c\u7528\u6279\u5904\u7406\u65f6\u7684\u6279\u6b21\u6821\u6b63<\/span><\/span><\/p>\n\u5de6\u56fe\uff1a\u89e3\u91ca\u65b9\u5dee\u56fe\u3002\u5f53showplot=TRUE\u65f6\u663e\u793a\u9ed8\u8ba4\u56fe\u5f62\u3002\u8be5\u56fe\u8868\u793a\u4e3a\u89e3\u91ca\u611f\u5174\u8da3\u6548\u5e94\uff08\u6279\u6b21\u6548\u5e94\uff09\u7684\u67d0\u79cd\u53d8\u5f02\u6027\uff08y\u8f74\uff09\u6240\u9700\u7684\u7ec4\u5206\u6570\u91cf\uff08x\u8f74\uff09\u3002\u6a21\u578b\u9009\u62e9\u7684\u7ec4\u5206\u6570\u91cf\u7528\u4e09\u89d2\u5f62\u7b26\u53f7\u8868\u793a\u3002\u7070\u8272\u7684\u865a\u7ebf\u8868\u793a\u7531Variability\u53c2\u6570\u7ed9\u51fa\u7684\u9608\u503c\uff08\u767e\u5206\u6bd4\uff09\u3002\u53f3\u56fe\uff1a\u4e0d\u8003\u8651\u6279\u6b21\u548c\u6761\u4ef6\u4e4b\u95f4\u7684\u4ea4\u4e92\u4f5c\u7528\u65f6\uff0c\u7ecf\u8fc7\u6821\u6b63\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684PCA\u56fe\u3002 <\/span> \u6839\u636e\u56fe2\u7684\u5de6\u56fe\uff0c\u5df2\u9009\u62e9\u4e24\u4e2a\u4e3b\u6210\u5206\uff08PCs\uff09\u6765\u89e3\u91ca\u6279\u6b21\u6548\u5e94\u603b\u53d8\u5f02\u7684\u81f3\u5c1195%\u3002\u53f3\u56fe\u663e\u793a\u4e86\u4f7f\u7528\u8fd9\u79cd\u5206\u6790\u5bf9\u4fee\u6b63\u540e\u7684\u6570\u636e\u8fdb\u884cPCA\u3002\u73b0\u5728\u6570\u636e\u4e2d\u7684\u4e3b\u8981\u53d8\u5f02\u6e90\uff08PC1)\u7531\u5b9e\u9a8c\u6761\u4ef6\u51b3\u5b9a\uff0c\u800c\u6837\u672c\u4e0d\u518d\u6309\u6279\u6b21\u805a\u7c7b\u3002<\/span><\/span> <\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code>par(mfrow =c(1<\/span>,2<\/span>)) <\/span><\/code><code>arsyn_2 <-ARSyNbac(data_RNA, modelName =\"RNA\"<\/span>, Variability =0.95<\/span>, <\/span><\/code><code> batchEstimation =TRUE<\/span>, filterNoise =FALSE<\/span>, Interaction =TRUE<\/span>) <\/span><\/code><code>plot(arsyn_2, typeP=\"pca.cor\"<\/span>, bty =\"L\"<\/span>, <\/span><\/code><code> pch = custom_pch, cex =3<\/span>, col.per.group = custom_col, <\/span><\/code><code> legend.text =c(\"Color: Batch\"<\/span>, names(data_RNA$ListOfBatches), <\/span><\/code><code> \"Fill: Cond.\"<\/span>, unique(colData(data_RNA$ListOfBatches$A)$tfactor)), <\/span><\/code><code> args.legend =list<\/span>(\"x\"<\/span>=\"topright\"<\/span>, <\/span><\/code><code> \"pch\"<\/span>=c(NA, 15<\/span>, 15<\/span>, 15<\/span>, <\/span><\/code><code> NA, 15<\/span>, 0<\/span>), <\/span><\/code><code> \"col\"<\/span>=c(NA, \"brown2\"<\/span>, \"dodgerblue\"<\/span>, \"forestgreen\"<\/span>, <\/span><\/code><code> NA, 1<\/span>, 1<\/span>), <\/span><\/code><code> \"bty\"<\/span>=\"n\"<\/span>, <\/span><\/code><code> \"cex\"<\/span>=1.2<\/span>))<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" loading=\"lazy\" data-imgfileid=\"100014468\" data-ratio=\"0.5611111111111111\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_9aJMHw2RaqO0xYl0MLnicgxQgpk1sg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSIgiadnPnKkHibsAeJvcU7ibqnNOf9aJMHw2RaqO0xYl0MLnicgxQgpk1sg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"314.0000305175781\" width=\"560.010009765625\" class=\"rich_pages wxw-img\" \/><\/span> <\/span>\u56fe3\uff1a<\/span>\u4ea4\u4e92\u4f5c\u7528=TRUE\u65f6\u7684\u6279\u6b21\u6821\u6b63<\/span><\/span><\/p>\n\u5de6\u56fe\uff1a\u65b9\u5dee\u89e3\u91ca\u56fe\u3002\u5f53showplot=TRUE\u65f6\uff0c\u9ed8\u8ba4\u663e\u793a\u6b64\u56fe\u3002\u8be5\u56fe\u8868\u793a\u4e3a\u4e86\u89e3\u91ca\u611f\u5174\u8da3\u7684\u6548\u5e94\uff08\u6279\u6b21\u6548\u5e94\uff09\u7684\u67d0\u4e00\u90e8\u5206\uff08y\u8f74\uff09\u6240\u9700\u7684\u7ec4\u5206\u6570\u91cf\uff08x\u8f74\uff09\u3002\u6a21\u578b\u4e2d\u6240\u9009\u62e9\u7684\u7ec4\u5206\u6570\u91cf\u7528\u4e09\u89d2\u5f62\u7b26\u53f7\u8868\u793a\u3002\u7070\u8272\u7684\u865a\u7ebf\u8868\u793a\u7531Variability\u53c2\u6570\uff08\u4ee5\u767e\u5206\u6bd4\u5f62\u5f0f\uff09\u7ed9\u51fa\u7684\u9608\u503c\u3002 \u53f3\u56fe\uff1a\u7ecf\u8fc7\u6279\u6b21\u6761\u4ef6\u4ea4\u4e92\u6821\u6b63\u540e\u7684\u57fa\u56e0\u8868\u8fbePCA\u56fe\u8c31\u3002 \u5728\u56fe3\uff08\u53f3\u4fa7\u9762\u677f\uff09\u4e2d\uff0cPC1\u4e3a\u8d1f\u7684\u6240\u6709\u70b9\u90fd\u5bf9\u5e94\u4e8eGlu-\u6837\u672c\uff0c\u800cPC1\u4e3a\u6b63\u7684\u6240\u6709\u70b9\u5bf9\u5e94\u4e8eGlu+\u6837\u672c\uff0c\u6b63\u5982\u5728\u6a21\u578b\u4e2d\u4e0d\u5305\u62ec\u76f8\u4e92\u4f5c\u7528\u65f6\u6240\u53d1\u751f\u7684\u60c5\u51b5\u4e00\u6837\uff08\u56fe2\uff0c\u53f3\u4fa7\u9762\u677f\uff09\u3002\u7136\u800c\uff0c\u5728\u6b64\u7b2c\u4e8c\u6a21\u578b\u4e2d\uff0cPC1\u5bf9\u6570\u636e\u53d8\u5f02\u6027\u7684\u89e3\u91ca\u767e\u5206\u6bd4\u66f4\u9ad8\uff0c\u8868\u660e\u6279\u6b21\u6548\u5e94\u6821\u6b63\u6548\u679c\u66f4\u597d\u3002\u4e00\u822c\u6765\u8bf4\uff0c\u6211\u4eec\u5efa\u8bae\u4f7f\u7528\u9ed8\u8ba4\u53c2\u6570\uff08Interaction=FALSE)\uff0c\u56e0\u4e3a\u5c06\u90e8\u5206\u4fe1\u53f7\u89c6\u4e3a\u6279\u6b21\u6548\u5e94\u53ef\u80fd\u5bfc\u81f4\u6240\u9700\u4fe1\u53f7\u7684\u6548\u679c\u88ab\u7a00\u91ca\u3002\u4f46\u662f\uff0c\u6279\u6b21\u548c\u5b9e\u9a8c\u6761\u4ef6\u4e4b\u95f4\u7684\u76f8\u4e92\u4f5c\u7528\u6709\u65f6\u53ef\u80fd\u5f88\u5f3a\u70c8\uff0c\u56e0\u6b64\u6211\u4eec\u5e94\u8be5\u8003\u8651\u5c06\u76f8\u4e92\u4f5c\u7528\u5305\u62ec\u5728\u6a21\u578b\u4e2d\uff0c\u4ee5\u66f4\u597d\u5730\u6821\u6b63\u6570\u636e\u3002 \u56fe1\u3001\u56fe2\u548c\u56fe3\u4e2d\u7684PCA\u56fe\u662f\u7531MultiBaC\u5305\u4e2d\u7684\u81ea\u5b9a\u4e49plot\u51fd\u6570\u751f\u6210\u7684\u3002\u6709\u5173\u6b64\u51fd\u6570\u7684\u66f4\u591a\u8be6\u7ec6\u4fe1\u606f\uff0c\u8bf7\u5728\u201cARSyN\u548cMultiBaC\u7ed3\u679c\u7684\u89c6\u89c9\u5448\u73b0\u201d\u90e8\u5206\u67e5\u627e\uff0c\u5176\u4e2d\u5b8c\u6574\u63cf\u8ff0\u4e86plot\u51fd\u6570\u7684\u6240\u6709\u53c2\u6570\u3002<\/span> <\/span><o:page><\/o:page><\/p>\nARSyNbac\u53bb\u566a<\/strong><\/span><\/p>\n\u5f53batch\u672a\u88ab\u8bc6\u522b\u65f6\uff0c<\/span>ARSyNbac<\/span>\u901a\u8fc7\u8bbe\u7f6e<\/span>batchEstimation = FALSE<\/span>\u548c<\/span>filterNoise = TRUE<\/span>\u5bf9\u6b8b\u5dee\u4e2d\u7cfb\u7edf\u566a\u58f0\u7684\u5b58\u5728\u8fdb\u884c\u5206\u6790\u3002<\/span><\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code>par(mfrow =c(1<\/span>,2<\/span>)) <\/span><\/code><code>arsyn_3 <-ARSyNbac(data_RNA, modelName =\"RNA\"<\/span>, beta =0.5<\/span>, <\/span><\/code><code> batchEstimation =FALSE<\/span>, filterNoise =TRUE<\/span>) <\/span><\/code><code>plot(arsyn_3, typeP=\"pca.cor\"<\/span>, bty =\"L\"<\/span>, <\/span><\/code><code> pch = custom_pch, cex =3<\/span>, col.per.group = custom_col, <\/span><\/code><code> legend.text =c(\"Color: Batch\"<\/span>, names(data_RNA$ListOfBatches), <\/span><\/code><code> \"Fill: Cond.\"<\/span>, unique(colData(data_RNA$ListOfBatches$A)$tfactor)), <\/span><\/code><code> args.legend =list<\/span>(\"x\"<\/span>=\"topright\"<\/span>, <\/span><\/code><code> \"pch\"<\/span>=c(NA, 15<\/span>, 15<\/span>, 15<\/span>, <\/span><\/code><code> NA, 15<\/span>, 0<\/span>), <\/span><\/code><code> \"col\"<\/span>=c(NA, \"brown2\"<\/span>, \"dodgerblue\"<\/span>, \"forestgreen\"<\/span>, <\/span><\/code><code> NA, 1<\/span>, 1<\/span>), <\/span><\/code><code> \"bty\"<\/span>=\"n\"<\/span>, <\/span><\/code><code> \"cex\"<\/span>=1.2<\/span>)) <\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014464\" data-ratio=\"0.5611111111111111\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_zgInvjRdiadJjBDzrk7KOeswjNVnhg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVScszXMnNJxkqbE0GtrCcfXz7umzgInvjRdiadJjBDzrk7KOeswjNVnhg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"314.3999938964844\" width=\"560.010009765625\" \/><\/span><span style=\"font-family: mp-quote, -apple-system-font, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Hiragino Sans GB", "Microsoft YaHei UI", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 0.034em;text-align: justify;font-size: 15px;\"> <\/span><\/span> <\/p>\n\u56fe4\uff1a<\/span>\u566a\u58f0\u51cf\u5c11\u6a21\u5f0f<\/span> <\/span><\/span><\/p>\n\u5de6\uff1a\u65b9\u5dee\u89e3\u91ca\u56fe\u3002\u5f53 showplot = TRUE \u65f6\uff0c\u9ed8\u8ba4\u7ed8\u5236\u8be5\u56fe\u3002\u5b83\u8868\u793a\u6b8b\u5dee\u4e2d\u53ef\u53d8\u6027\u7684\u767e\u5206\u6bd4\uff08y \u8f74\uff09\uff0c\u7531\u5177\u6709\u7ed9\u5b9a\u4e3b\u6210\u5206\u6570\u76ee\u7684\u6a21\u578b\u89e3\u91ca\uff08x \u8f74\uff09\u3002\u6700\u7ec8\u6a21\u578b\u4e2d\u9009\u62e9\u7684\u7ec4\u4ef6\u6570\u7528\u4e09\u89d2\u5f62\u7b26\u53f7\u8868\u793a\uff0c\u5e76\u8ba1\u7b97\u4e3a\u89e3\u91ca beta \u500d\u6b8b\u5dee\u5e73\u5747\u53ef\u53d8\u6027\u3002\u53f3\uff1a\u4fee\u6b63\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684 PCA \u56fe\u3002 \u5728\u30104\u3011\u56fe\u4e2d\uff0c\u6211\u4eec\u53ef\u4ee5\u770b\u5230\uff0c\u5c3d\u7ba1\u8fd9\u4e2a\u6279\u6b21\u88ab\u8ba4\u4e3a\u662f\u4e0d\u660e\u786e\u7684(batchEstimation=FALSE)\uff0c\u4f46\u662fARSyN\u5df2\u7ecf\u901a\u8fc7\u4f30\u8ba1\u4e0d\u9700\u8981\u53d8\u5316\u7684\u4e3b\u8981\u6765\u6e90\uff0c\u4ece\u6570\u636e\u4e2d\u6d88\u9664\u4e86\u566a\u58f0\u3002\u5728\u8fd9\u79cd\u566a\u58f0\u51cf\u5c11\u6a21\u5f0f\u4e0b\uff0c\u6211\u4eec\u53ef\u4ee5\u901a\u8fc7beta\u53c2\u6570\u6765\u8c03\u6574\u6b8b\u5dee\u4e2d\u5269\u4f59\u566a\u58f0\u7684\u5e45\u5ea6\u3002\u57fa\u672c\u4e0a\uff0c\u8d85\u8fc7beta\u500d\u7684\u5e73\u5747\u53d8\u5f02\u6027\u7684\u6210\u5206\u88ab\u786e\u5b9a\u4e3a\u6b8b\u5dee\u4e2d\u7684\u7cfb\u7edf\u566a\u58f0(\u5728\u8fd9\u4e2a\u6a21\u578b\u4e2d\u9009\u62e9\u4e863\u4e2a\u6210\u5206)\u3002\u56e0\u6b64\uff0cbeta\u503c\u8d8a\u5927\uff0c\u5bfc\u81f4\u6b8b\u5dee\u4e2d\u9009\u62e9\u66f4\u5c11\u7684\u6210\u5206\u3002<\/span><\/span><\/p>\nARSyNbac\u4e24\u79cd\u6a21\u5f0f<\/strong><\/span><\/p>\n\u5982\u679c\u6279\u6b21\u6548\u5e94\u7684\u6765\u6e90\u5df2\u77e5\uff0c\u4f46\u53ef\u80fd\u5b58\u5728\u4e00\u4e2a\u989d\u5916\u7684\u672a\u77e5\u7684\u4e0d\u9700\u8981\u7684\u53d8\u5f02\u6e90\uff0c<\/span>ARSyNbac<\/span>\u53ef\u4ee5\u901a\u8fc7\u8bbe\u7f6e<\/span>batchEstimation = TRUE<\/span>\u548c<\/span>filterNoise = TRUE<\/span>\u6765\u6267\u884c\u524d\u4e24\u79cd\u65b9\u6cd5\u3002\u8bf7\u6ce8\u610f\uff0c\u5982\u679c\u5df2\u77e5\u7684\u6279\u6b21\u6548\u5e94\u5e76\u4e0d\u4ee3\u8868\u6211\u4eec\u6570\u636e\u4e2d\u7684\u4e3b\u8981\u566a\u58f0\u6e90\uff0c\u8fd9\u79cd\u6a21\u5f0f\u4e5f\u53ef\u80fd\u662f\u6709\u7528\u7684\u3002<\/span><\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code>par(mfrow =c(1<\/span>,2<\/span>)) <\/span><\/code><code>arsyn_4 <-ARSyNbac(data_RNA, modelName =\"RNA\"<\/span>, beta =0.5<\/span>, <\/span><\/code><code> batchEstimation =TRUE<\/span>, filterNoise =TRUE<\/span>, <\/span><\/code><code> Interaction =TRUE<\/span>, <\/span><\/code><code> Variability =0.95<\/span>) <\/span><\/code><code>plot(arsyn_4, typeP=\"pca.cor\"<\/span>, bty =\"L\"<\/span>, <\/span><\/code><code> pch = custom_pch, cex =3<\/span>, col.per.group = custom_col, <\/span><\/code><code> legend.text =c(\"Color: Batch\"<\/span>, names(data_RNA$ListOfBatches), <\/span><\/code><code> \"Fill: Cond.\"<\/span>, unique(colData(data_RNA$ListOfBatches$A)$tfactor)), <\/span><\/code><code> args.legend =list<\/span>(\"x\"<\/span>=\"topright\"<\/span>, <\/span><\/code><code> \"pch\"<\/span>=c(NA, 15<\/span>, 15<\/span>, 15<\/span>, <\/span><\/code><code> NA, 15<\/span>, 0<\/span>), <\/span><\/code><code> \"col\"<\/span>=c(NA, \"brown2\"<\/span>, \"dodgerblue\"<\/span>, \"forestgreen\"<\/span>, <\/span><\/code><code> NA, 1<\/span>, 1<\/span>), <\/span><\/code><code> \"bty\"<\/span>=\"n\"<\/span>, <\/span><\/code><code> \"cex\"<\/span>=1.2<\/span>))<\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\"><\/span><o:page><\/o:page><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014470\" data-ratio=\"0.5611111111111111\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_ibNkicYVbDVCHvAzVOrytCPbhiaZXg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSHbYevicvvA7mbPAf8bw4XACfVpN4ibNkicYVbDVCHvAzVOrytCPbhiaZXg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"313.9999694824219\" width=\"560.010009765625\" \/><\/span> <\/span>\u56fe5\uff1a<\/span>\u4e24\u79cd\u6a21\u5f0f\u7ed3\u5408<\/span><\/span><\/p>\n<p style=\"margin-top: 9.0pt;margin-bottom: 9.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\">\u5de6\u56fe\uff1a\u65b9\u5dee\u89e3\u91ca\u56fe\u3002\u5f53 showplot = TRUE \u65f6\uff0c\u9ed8\u8ba4\u663e\u793a\u8be5\u56fe\u3002\u56fe\u4e2d\u8868\u793a\u7684\u662f\u67d0\u4e00\u6a21\u578b\u5bf9\u6b8b\u5dee\u53d8\u5f02\u7684\u89e3\u91ca\u767e\u5206\u6bd4\uff08y\u8f74\uff09\uff0c\u968f\u7740\u4e3b\u6210\u5206\u6570\u76ee\u7684\u589e\u52a0\uff08x\u8f74\uff09\u3002\u6700\u7ec8\u6a21\u578b\u6240\u9009\u5b9a\u7684\u4e3b\u6210\u5206\u6570\u76ee\u7528\u4e09\u89d2\u5f62\u7b26\u53f7\u8868\u793a\uff0c\u5e76\u8ba1\u7b97\u89e3\u91cabeta\u500d\u6b8b\u5dee\u53d8\u5f02\u7684\u5e73\u5747\u503c\u3002<\/span><\/p>\n<p style=\"margin-top: 9.0pt;margin-bottom: 9.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\">\u53f3\u56fe\uff1a\u4fee\u6b63\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684PCA\u56fe\u3002 \u5728\u56fe5\u4e2d\uff0c\u6211\u4eec\u53ef\u4ee5\u770b\u5230\uff0c\u540c\u65f6\u6267\u884c\u4e24\u79cd\u65b9\u6cd5\u65f6\uff0cARSyNbac\u8fbe\u5230\u4e86PC1\u65b9\u5dee\u7684\u6700\u5927\u89e3\u91ca\u7387\uff08\u7279\u522b\u662f\u4e0e\u56fe3\u76f8\u6bd4\uff09\u3002\u5728\u8fd9\u79cd\u6a21\u5f0f\u4e0b\uff0c\u6211\u4eec\u53ef\u4ee5\u5229\u7528\u03b2\u53c2\u6570\u548c\u4e0e\u89e3\u91ca\u65b9\u5dee\u76f8\u5173\u7684\u6279\u6b21\u6548\u5e94\u6765\u8c03\u6574\u6b8b\u5dee\u566a\u58f0\u53bb\u9664\u7684\u7a0b\u5ea6\u3002\u5728\u8fd9\u4e2a\u4f8b\u5b50\u4e2d\uff0c\u5982\u56fe4\u6240\u793a\uff0c\u5df2\u77e5\u6279\u6b21\u6548\u5e94\u662f\u4e3b\u8981\uff08\u51e0\u4e4e\u662f\u552f\u4e00\u7684\uff09\u4e0d\u9700\u8981\u7684\u53d8\u5f02\u6e90\u3002\u56e0\u6b64\uff0c\u5728\u5176\u4ed6\u5177\u6709\u591a\u4e2a\u6279\u6b21\u6e90\u7684\u60c5\u51b5\u4e0b\uff0c\u8fd9\u79cd\u6a21\u5f0f\u7684\u7ed3\u679c\u53ef\u80fd\u4e0e\u4e4b\u524d\u7684\u4e24\u79cd\u64cd\u4f5c\u65b9\u5f0f\u975e\u5e38\u4e0d\u540c\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n\u591a\u7ec4\u5b66\u6570\u636e\u96c6\u4e0a\u7684\u6279\u6b21\u6548\u5e94\u6821\u6b63<\/strong><\/span><\/p>\n\u5173\u4e8eMultiBaC<\/strong><\/span><\/p>\nMultiBaC \u65b9\u6cd5\u6982\u8ff0<\/span><\/p>\nMultiBaC\u662f\u4e00\u79cd\u4ece\u591a\u7ec4\u5b66\u6570\u636e\u4e2d\u63a8\u65ad\u7ec6\u83cc\u7fa4\u843d\u8c03\u63a7\u903b\u8f91\u7684\u8ba1\u7b97\u65b9\u6cd5\u3002 \u591a\u7ec4\u5b66\u6570\u636e\u6574\u5408\u5df2\u6210\u4e3a\u7406\u89e3\u751f\u7269\u7cfb\u7edf\u5de5\u4f5c\u673a\u5236\u7684\u6d41\u884c\u65b9\u6cd5\u3002\u7136\u800c\uff0c\u751f\u6210\u8fd9\u7c7b\u6570\u636e\u96c6\u4ecd\u7136\u6210\u672c\u9ad8\u4e14\u8017\u65f6\u3002\u56e0\u6b64\uff0c\u975e\u5e38\u5e38\u89c1\u7684\u60c5\u51b5\u662f\uff0c\u5e76\u975e\u6240\u6709\u6837\u672c\u6216\u7ec4\u5b66\u6570\u636e\u7c7b\u578b\u540c\u65f6\u4ea7\u751f\u6216\u5728\u540c\u4e00\u5b9e\u9a8c\u5ba4\u4ea7\u751f\uff0c\u800c\u662f\u5206\u6279\u8fdb\u884c\u3002\u6b64\u5916\uff0c\u5f53\u7814\u7a76\u56e2\u961f\u65e0\u6cd5\u751f\u6210\u81ea\u5df1\u7684\u591a\u7ec4\u5b66\u6570\u636e\u96c6\u65f6\uff0c\u4ed6\u4eec\u901a\u5e38\u4ece\u4e0d\u540c\u7684\u516c\u5171\u5b58\u50a8\u5e93\u6536\u96c6\uff0c\u56e0\u6b64\u6765\u81ea\u4e0d\u540c\u7684\u7814\u7a76\u6216\u5b9e\u9a8c\u5ba4\uff08\u4e5f\u662f\u6765\u81ea\u4e0d\u540c\u7684\u6279\u6b21\uff09\u3002\u5728\u8fd9\u4e24\u79cd\u60c5\u51b5\u4e0b\uff0c\u90fd\u9700\u8981\u4e8b\u5148\u4ece\u8fd9\u4e9b\u6570\u636e\u96c6\u4e2d\u53bb\u9664\u6279\u6b21\u6548\u5e94\u4ee5\u6210\u529f\u8fdb\u884c\u6570\u636e\u6574\u5408\u3002\u7ea0\u6b63\u5355\u4e00\u6570\u636e\u7c7b\u578b\u7684\u6279\u6b21\u6548\u5e94\u7684\u65b9\u6cd5\u65e0\u6cd5\u5e94\u7528\u4e8e\u7ea0\u6b63\u8de8\u7ec4\u5b66\u7684\u6279\u6b21\u6548\u5e94\uff0c\u56e0\u6b64\u6211\u4eec\u5f00\u53d1\u4e86MultiBaC\u7b56\u7565\uff0c\u8be5\u7b56\u7565\u53ef\u7ea0\u6b63\u5206\u5e03\u5728\u4e0d\u540c\u5b9e\u9a8c\u5ba4\u6216\u6570\u636e\u91c7\u96c6\u4e8b\u4ef6\u4e2d\u7684\u591a\u7ec4\u5b66\u6570\u636e\u96c6\u4e2d\u7684\u6279\u6b21\u6548\u5e94\u3002 \u7136\u800c\uff0c\u5bf9\u4e8e\u591a\u7ec4\u5b66\u6570\u636e\u96c6\u6709\u4e00\u4e9b\u8981\u6c42\uff0c\u4ee5\u4fbf\u4f7f\u7528MultiBaC\u53bb\u9664\u8de8\u7ec4\u5b66\u7684\u6279\u6b21\u6548\u5e94\uff1a<\/span><\/p>\n\u2022\u6bcf\u4e2a\u6279\u6b21\u4e2d\u5fc5\u987b\u81f3\u5c11\u6709\u4e00\u79cd\u5e38\u89c1\u7ec4\u5b66\u6570\u636e\u7c7b\u578b\u3002\u4f8b\u5982\uff0c\u6211\u4eec\u53ef\u80fd\u5728\u6240\u6709\u6279\u6b21\u4e2d\u90fd\u6709\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u6d4b\u91cf\uff0c\u7136\u540e\u5728\u6bcf\u4e2a\u6279\u6b21\u4e2d\u5177\u6709\u5176\u4ed6\u4e0d\u540c\u7684\u7ec4\u5b66\u6570\u636e\u7c7b\u578b\u3002\u4e0d\u5fc5\u8981\u6c42\u4f7f\u7528\u76f8\u540c\u7684\u6280\u672f\u6765\u6d4b\u91cf\u5171\u540c\u7684\u7ec4\u5b66\uff08\u4f8b\u5982\u57fa\u56e0\u8868\u8fbe\uff09\u3002\u4f8b\u5982\uff0c\u6211\u4eec\u53ef\u4ee5\u6709\u4e00\u4e2a\u6279\u6b21\u4e2d\u7684\u5fae\u9635\u5217\u8868\u8fbe\u6570\u636e\u548c\u53e6\u4e00\u4e2a\u6279\u6b21\u4e2d\u7684RNA-seq\u6570\u636e\u3002<\/span><\/p>\n\u2022\u5bf9\u4e8e\u6240\u6709\u5e38\u89c1\u6570\u636e\u77e9\u9635\uff0c\u7ec4\u5b66\u7279\u5f81\u6807\u8bc6\u7b26\u5fc5\u987b\u76f8\u540c\u3002\u4f8b\u5982\uff0c\u6211\u4eec\u4e0d\u80fd\u5728\u4e00\u4e2a\u6279\u6b21\u4e2d\u4f7f\u7528Ensembl\u6807\u8bc6\u7b26\uff0c\u800c\u5728\u53e6\u4e00\u4e2a\u6279\u6b21\u4e2d\u4f7f\u7528RefSeq\u3002\u4e0d\u5fc5\u8981\u6c42\u6240\u6709\u6279\u6b21\u4e2d\u5177\u6709\u76f8\u540c\u6570\u91cf\u7684\u7ec4\u5b66\u7279\u5f81\uff0c\u4f8b\u5982\u57fa\u56e0\u3002MultiBac\u5c06\u4ece\u6240\u6709\u5e38\u89c1\u6570\u636e\u7c7b\u578b\u77e9\u9635\u4e2d\u63d0\u53d6\u516c\u5171\u6807\u8bc6\u7b26\u4ee5\u6267\u884c\u5206\u6790\u3002<\/span><\/p>\n\u2022\u5728\u540c\u4e00\u6279\u6b21\u4e2d\uff0c\u5b9e\u9a8c\u8bbe\u8ba1\u5bf9\u4e8e\u8be5\u6279\u6b21\u4e2d\u7684\u6240\u6709\u7ec4\u5b66\u90fd\u5fc5\u987b\u76f8\u540c\uff0c\u5373\u76f8\u540c\u7684\u5b9e\u9a8c\u7ec4\uff0c\u5177\u6709\u76f8\u540c\u6570\u91cf\u7684\u6765\u81ea\u76f8\u540c\u4e2a\u4f53\u7684\u91cd\u590d\u3002\u6240\u6709\u8fd9\u4e9b\u6837\u672c\u5728\u6240\u6709\u7ec4\u5b66\u6570\u636e\u77e9\u9635\u4e2d\u90fd\u5fc5\u987b\u4ee5\u76f8\u540c\u7684\u987a\u5e8f\u6392\u5217\u3002<\/span><\/p>\n\u793a\u4f8b\uff1a\u9175\u6bcd\u591a\u7ec4\u5b66\u6570\u636e\u96c6<\/strong><\/span><\/p>\n\u8fd9\u4e9b\u6570\u636e\u5305\u62ec\u57fa\u56e0\u8868\u8fbe\u6570\u636e\uff08RNA\uff09\uff0c\u4ee5\u53ca\u7531\u4e0d\u540c\u5b9e\u9a8c\u5ba4\u5206\u522b\u4ea7\u751f\u7684\u4e0d\u540c\u5176\u4ed6\u7ec4\u5b66\u6570\u636e\u7c7b\u578b\u3002\u5b9e\u9a8c\u5ba4A\u6536\u96c6\u4e86\u8f6c\u5f55\u901f\u7387\u6570\u636e\uff08GRO\uff0c\u5b58\u53d6\u53f7GSE1002\uff09[<\/span>2<\/span>]\u3002\u5b9e\u9a8c\u5ba4B\u83b7\u5f97\u4e86\u7ffb\u8bd1\u901f\u7387\u6570\u636e\uff08RIBO\uff0c\u5b58\u53d6\u53f7GSE56622\uff09[<\/span>5<\/span>]\u3002\u6700\u540e\uff0c\u5b9e\u9a8c\u5ba4C\u6d4b\u91cf\u4e86\u5168\u5c40PAR-CLIP\u6570\u636e\uff08PAR-CLIP\uff0c\u5b58\u53d6\u53f7GSE43747\uff09[<\/span>6<\/span>]\u3002\u56e0\u6b64\uff0c\u8fd9\u4e9b\u5b9e\u9a8c\u5ba4\u5171\u4eab\u4e00\u4e2a\u6570\u636e\u7c7b\u578b\uff08RNA\uff09\uff0c\u800c\u5176\u4ed6\u6570\u636e\u7c7b\u578b\u5219\u5404\u4e0d\u76f8\u540c\uff08GRO\u3001RIBO\u548cPAR-CLIP\uff09\u3002\u8fd9\u79cd\u5206\u5e03\u5f0f\u591a\u7ec4\u5b66\u65b9\u6848\u4ee3\u8868\u4e86MultiBaC\u6240\u89e3\u51b3\u7684\u6821\u6b63\u95ee\u9898\u3002\u6570\u636e\u7ed3\u6784\u7684\u793a\u610f\u56fe\u53ef\u89c1\u4e8e\u56fe <\/span>6<\/span>\u3002 <img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014469\" data-ratio=\"0.4675925925925926\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_PFOIdFy6bZ8PUeLf9IHVFxFLib8NWg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSMCfw48LfobHuUPKMXHxRPLRTIPFOIdFy6bZ8PUeLf9IHVFxFLib8NWg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"262.0\" width=\"560.010009765625\" \/> <\/span>\u56fe6\uff1a<\/span>\u9175\u6bcd\u4f8b\u6570\u636e\u7ed3\u6784\u7684\u65b9\u6848<\/span><\/span><\/p>\n\u6b64\u9175\u6bcd\u591a\u7ec4\u5b66\u6570\u636e\u5305\u542b\u5728<\/span><span style=\"font-size: 15px;letter-spacing: 0.034em;font-family: Cambria;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;font-weight: bold;\">MutiBaC<\/span>\u5305\u4e2d\uff0c\u7528\u6765\u8bf4\u660e\u6b64\u5305\u7684\u4f7f\u7528\u65b9\u6cd5\u3002\u8fd9\u516d\u4e2a\u77e9\u9635\u53ef\u4ee5\u901a\u8fc7\u4f7f\u7528 <\/span><span style=\"font-size: 15px;letter-spacing: 0.034em;font-family: Cambria;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;font-style: italic;\">data(\u201cmultiyeast\u201d)<\/span>\u6307\u4ee4\u6765\u52a0\u8f7d\u3002<\/span><\/p>\nMultiBaC\u8f93\u5165\u6570\u636e<\/strong><\/span><\/p>\n\u5982\u524d\u6240\u8ff0\uff0c<\/span>MultiBaC<\/span>\u5305\u4f7f\u7528<\/span>MultiAssayExperiment<\/span>\u5bf9\u8c61\uff0c\u8fd9\u662fBioconductor\u4e2d\u7528\u4e8e\u591a\u7ec4\u5b66\u7814\u7a76\u7684\u4e00\u79cd\u5bb9\u5668\u7c7b\u578b\uff0c\u53ef\u4ee5\u4ece\u4e00\u4e2a\u7531\u77e9\u9635\u6216<\/span>data.frame<\/span>\u5bf9\u8c61\u7ec4\u6210\u7684\u5217\u8868\u4e2d\u521b\u5efa\u3002\u8fd9\u4e9b\u77e9\u9635\u5fc5\u987b\u5177\u6709\u4ee5\u884c\u4e3a\u7279\u5f81\u3001\u4ee5\u5217\u4e3a\u6837\u672c\u7684\u7279\u70b9\uff08\u8bf7\u53c2\u89c1ARSyNbac\u90e8\u5206\u4e2d\u7684\u793a\u4f8b\uff09\u3002\u7531\u4e8e<\/span>MultiBaC<\/span>\u5728\u76f8\u540c\u6279\u6b21\u7684\u4e0d\u540c\u7ec4\u5b66\u4e4b\u95f4\u8ba1\u7b97\u56de\u5f52\u6a21\u578b\uff0c\u56e0\u6b64\u91cd\u8981\u7684\u662f\u6765\u81ea\u76f8\u540c\u6279\u6b21\u7684\u6240\u6709\u77e9\u9635\u5fc5\u987b\u5177\u6709\u76f8\u540c\u7684\u5b9e\u9a8c\u8bbe\u8ba1\uff1a\u76f8\u540c\u6570\u91cf\u7684\u6837\u672c\u5e76\u4ee5\u76f8\u540c\u7684\u987a\u5e8f\u6392\u5217\u3002<\/span>MultiBaC<\/span>\u4e5f\u6d89\u53ca\u4e0d\u540c\u6279\u6b21\u7684\u4e0d\u540c\u7ec4\u5b66\u7684\u5171\u4fe1\u606f\u3002\u56e0\u6b64\uff0c\u5982\u679c\u7ec4\u5b66\u53d8\u91cf\u7684\u6570\u91cf\u548c\u987a\u5e8f\u4e0d\u540c\uff0c\u5219<\/span>MultiBaC<\/span>\u5c06\u9009\u62e9\u5171\u6709\u7684\u53d8\u91cf\u7528\u4e8e\u6a21\u578b\u3002\u56e0\u6b64\uff0c\u5fc5\u987b\u4f7f\u7528\u76f8\u540c\u7c7b\u578b\u7684\u6807\u8bc6\u7b26\u5bf9\u884c\u8fdb\u884c\u547d\u540d\u3002 \u8981\u751f\u6210\u4f5c\u4e3aMultiBaC\u51fd\u6570\u8f93\u5165\u7684<\/span>mbac<\/span>\u5bf9\u8c61\uff0c\u53ef\u4ee5\u4f7f\u7528\u5305\u4e2d\u7684<\/span>createMbac<\/span>\u51fd\u6570\uff0c\u8f7b\u677e\u4fbf\u6377\u5730\u5b8c\u6210\u8fd9\u9879\u4efb\u52a1\u3002<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"swift\"><code>my_mbac <- createMbac (inputOmics = list(A<\/span>.rna, A<\/span>.gro, <\/span><\/code><code> B<\/span>.rna, B<\/span>.ribo, <\/span><\/code><code> C<\/span>.rna, C<\/span>.par), <\/span><\/code><code> batchFactor = c<\/span>(\"A\"<\/span>, \"A\"<\/span>, <\/span><\/code><code> \"B\"<\/span>, \"B\"<\/span>, <\/span><\/code><code> \"C\"<\/span>, \"C\"<\/span>), <\/span><\/code><code> experimentalDesign = list(\"A\"<\/span> = c<\/span>(\"Glu+\"<\/span>, \"Glu+\"<\/span>, <\/span><\/code><code> \"Glu+\"<\/span>, \"Glu-\"<\/span>, <\/span><\/code><code> \"Glu-\"<\/span>, \"Glu-\"<\/span>), <\/span><\/code><code> \"B\"<\/span> = c<\/span>(\"Glu+\"<\/span>, \"Glu+\"<\/span>, <\/span><\/code><code> \"Glu-\"<\/span>, \"Glu-\"<\/span>), <\/span><\/code><code> \"C\"<\/span> = c<\/span>(\"Glu+\"<\/span>, \"Glu+\"<\/span>, <\/span><\/code><code> \"Glu-\"<\/span>, \"Glu-\"<\/span>)), <\/span><\/code><code> omicNames = c<\/span>(\"RNA\"<\/span>, \"GRO\"<\/span>, <\/span><\/code><code> \"RNA\"<\/span>, \"RIBO\"<\/span>, <\/span><\/code><code> \"RNA\"<\/span>, \"PAR\"<\/span>)) <\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\"><\/span><o:page><\/o:page><\/p>\n\u6709\u5173\u201ccreateMbac\u201d\u51fd\u6570\u7684\u66f4\u591a\u8be6\u7ec6\u4fe1\u606f\uff0c\u8bf7\u53c2\u89c1ARSyNbac\u8f93\u5165\u6570\u636e\u90e8\u5206\u3002\u9700\u8981\u6ce8\u610f\u7684\u662f\uff0c\u6211\u4eec\u4e0d\u9700\u8981\u6307\u660e\u54ea\u4e2a\u662f\u5e38\u89c1\u7684omic\uff08\u5728commonOmic\u53c2\u6570\u4e2d\uff09\uff0c\u56e0\u4e3a\u5bf9\u4e8e\u6240\u6709\u6279\u6b21\uff08\u5b9e\u9a8c\u5ba4\uff09\u6765\u8bf4\uff0c\u53ea\u6709\u4e00\u4e2a\u5171\u540c\u7684omic\uff08RNA\uff09\uff0c\u5e76\u4e14\u8be5\u51fd\u6570\u5c06\u5176\u68c0\u6d4b\u4e3a\u5e38\u89c1\u7684omic\u3002<\/span><\/p>\nMultiBaC correction<\/strong><\/span><\/p>\n\u4e00\u65e6\u4f7f\u7528\u201ccreateMbac\u201d\u51fd\u6570\u521b\u5efa\u4e86<\/span>mbac<\/span>\u5bf9\u8c61\uff0c\u5c31\u53ef\u4ee5\u5c06\u5176\u7528\u4f5c\u201cMultiBaC\u201d\u51fd\u6570\u7684\u8f93\u5165\u6570\u636e\uff08\u4ee5<\/span>mbac<\/span>\u53c2\u6570\u7684\u5f62\u5f0f\uff09\uff0c\u800c\u201cMultiBaC\u201d\u51fd\u6570\u662f\u7528\u4e8e\u6821\u6b63\u591a\u7ec4\u5b66\u6279\u6b21\u6548\u5e94\u7684\u5305\u88c5\u51fd\u6570\u3002<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code>MultiBaC (mbac, <\/span><\/code><code> test.comp = NULL<\/span>, scale = FALSE<\/span>, <\/span><\/code><code> center = TRUE<\/span>, crossval = NULL<\/span>, <\/span><\/code><code> Interaction = FALSE<\/span>, <\/span><\/code><code> Variability = 0.90<\/span>, <\/span><\/code><code> showplot = TRUE<\/span>, <\/span><\/code><code> showinfo = TRUE<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\"><span style=\"font-size: 15px;letter-spacing: 0.034em;text-align: justify;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;font-style: italic;\">MultiBaC<\/span>\u51fd\u6570\u7684\u53c2\u6570\u5bf9\u5e94\u4e8eMultiBaC\u65b9\u6cd5\u7684\u5404\u4e2a\u6b65\u9aa4\uff1a<\/span><\/span><\/p>\n\u2022<\/span>mbac<\/span>: \u7531 <\/span>createMbac<\/span> \u751f\u6210\u7684 mbac \u5bf9\u8c61\u3002<\/span><\/span><\/p>\n\u2022<\/span>test.comp<\/span>: PLS \u6a21\u578b\u5141\u8bb8\u7684\u6700\u5927\u7ec4\u4ef6\u6570\u3002\u5982\u679c\u4e3a NULL\uff08\u9ed8\u8ba4\uff09\uff0c\u5219\u4f7f\u7528\u77e9\u9635\u7684\u6700\u5c0f\u6709\u6548\u79e9\u4f5c\u4e3a\u6700\u5927\u7ec4\u4ef6\u6570\u3002<\/span><\/span><\/p>\n\u2022<\/span>scale<\/span>: \u903b\u8f91\u503c\u3002\u662f\u5426\u9700\u8981\u5bf9 X \u548c Y \u77e9\u9635\u8fdb\u884c\u7f29\u653e\u3002\u9ed8\u8ba4\u503c\u4e3a FALSE\u3002<\/span><\/span><\/p>\n\u2022<\/span>center<\/span>: \u903b\u8f91\u503c\u3002\u662f\u5426\u9700\u8981\u5bf9 X \u548c Y \u77e9\u9635\u8fdb\u884c\u4e2d\u5fc3\u5316\u3002\u9ed8\u8ba4\u503c\u4e3a TRUE\u3002<\/span><\/span><\/p>\n\u2022<\/span>crossval<\/span>: \u6574\u6570\uff1a\u4ea4\u53c9\u9a8c\u8bc1\u6bb5\u6570\u3002\u6837\u672c\u6570\uff08\u201cx\u201d\u7684\u884c\u6570\uff09\u5fc5\u987b >= crossvalI\u3002\u5982\u679c\u4e3a NULL\uff08\u9ed8\u8ba4\uff09\uff0c\u5219\u6267\u884c leave-one-out \u4ea4\u53c9\u9a8c\u8bc1\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n\u2022<\/span>Interaction<\/span>: \u903b\u8f91\u503c\u3002\u662f\u5426\u5728 ARSyN \u6a21\u578b\u4e2d\u5efa\u7acb\u5b9e\u9a8c\u56e0\u7d20\u548c\u6279\u6b21\u56e0\u7d20\u4e4b\u95f4\u7684\u76f8\u4e92\u4f5c\u7528\u6a21\u578b\u3002\u9ed8\u8ba4\u503c\u4e3a FALSE\u3002<\/span><\/span><\/p>\n\u2022<\/span>Variability<\/span>: \u4ece 0 \u5230 1 \u7684\u6700\u5c0f\u767e\u5206\u6bd4\u6570\u636e\u53d8\u5316\u6027\uff0c\u5bf9\u4e8e\u6bcf\u4e2a ARSyN \u6a21\u578b\u5fc5\u987b\u89e3\u91ca\u3002\u9ed8\u8ba4\u503c\u4e3a 0.90\u3002<\/span><\/span><\/p>\n\u2022<\/span>showplot<\/span>: \u903b\u8f91\u503c\u3002\u5982\u679c\u4e3a TRUE\uff08\u9ed8\u8ba4\uff09\uff0c\u5219\u663e\u793a Q2 \u548c\u89e3\u91ca\u65b9\u5dee\u56fe\u3002<\/span><\/span><\/p>\n\u2022<\/span>showinfo<\/span>: \u903b\u8f91\u503c\u3002\u5982\u679c\u4e3a TRUE\uff08\u9ed8\u8ba4\uff09\uff0c\u5219\u663e\u793a\u51fd\u6570\u8fdb\u5ea6\u4fe1\u606f\u3002 \u4e0b\u9762\u663e\u793a\u4e86\u4f7f\u7528MultiBaC\u51fd\u6570\u5bf9\u9175\u6bcd\u793a\u4f8b\u6570\u636e\u8fdb\u884c\u5904\u7406\u7684\u60c5\u51b5\uff1a<\/span><\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code>my_final_mbac <-MultiBaC (my_mbac, <\/span><\/code><code> test.comp =NULL, scale =FALSE, <\/span><\/code><code> center =TRUE, crossval =NULL, <\/span><\/code><code> Interaction =TRUE, <\/span><\/code><code> Variability =0.9, <\/span><\/code><code> showplot =TRUE, <\/span><\/code><code> showinfo =TRUE) <\/span><\/code><code>#<\/span># Step 1: Create PLS models <\/span><\/span><\/code><code>#<\/span># - Model for batch A <\/span><\/span><\/code><code>#<\/span># - Model for batch B <\/span><\/span><\/code><code>#<\/span># - Model for batch C <\/span><\/span><\/code><code>#<\/span># Step 2: Generating missing omics <\/span><\/span><\/code><code>#<\/span># Step 3: Batch effect correction using ARSyNbac <\/span><\/span><\/code><code>#<\/span># [1] \"Table: Inner correlation between scores for each PLS model computed.\" <\/span><\/span><\/code><code>#<\/span># <\/span><\/span><\/code><code>#<\/span># <\/span><\/span><\/code><code>#<\/span># A: GRO B: RIBO C: PAR <\/span><\/span><\/code><code>#<\/span># ------------- ---------- ---------- ---------- <\/span><\/span><\/code><code>#<\/span># Component: 1 0.9471967 0.9987790 0.9396986 <\/span><\/span><\/code><code>#<\/span># Component: 2 0.9277123 0.9991239 0.9998556 <\/span><\/span><\/code><code>#<\/span># Component: 3 0.9992129 1.0000000 1.0000000 <\/span><\/span><\/code><code>#<\/span># Component: 4 0.9999867 NA NA <\/span><\/span><\/code><code>#<\/span># Component: 5 1.0000000 NA NA <\/span><\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014471\" data-ratio=\"0.5611111111111111\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/10_um1skko71F9zbUNmLTgWxYTLhK3gqQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSxDhFxDldjkUocY1Dcf8GK0ayum1skko71F9zbUNmLTgWxYTLhK3gqQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"314.0\" width=\"560.010009765625\" \/><\/span> <\/span>\u56fe7\uff1a<\/span>Q2\u548c\u65b9\u5dee\u89e3\u91ca\u56fe<\/span><\/span><\/p>\n<p style=\"margin-top: 9.0pt;margin-bottom: 9.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\">Q2\u56fe\uff08\u5de6\uff09\u663e\u793a\u4e86\u8fbe\u5230\u4e00\u5b9aQ2\u503c\u6240\u9700\u7684\u7ec4\u4ef6\u6570\u91cf\uff08x\uff09\uff08y\uff09\u3002\u6bcf\u4e2a\u6a21\u578b\u6240\u9009\u7684\u7ec4\u4ef6\u6570\u91cf\u7528\u4e09\u89d2\u5f62\u7b26\u53f7\u8868\u793a\u3002\u7070\u8272\u7684\u865a\u7ebf\u8868\u793a0.7\u7684Q2\u9608\u503c\u3002\u65b9\u5dee\u89e3\u91ca\u56fe\uff08\u53f3\uff09\u8868\u793a\u4e86\u8981\u89e3\u91ca\u611f\u5174\u8da3\u7684\u6548\u5e94\uff08\u6279\u6b21\u6548\u5e94\uff09\u7684\u67d0\u4e2a\u53d8\u5f02\u6027\uff08y\uff09\u6240\u9700\u7684\u7ec4\u4ef6\u6570\u91cf\uff08x\uff09\u3002\u6bcf\u4e2a\u6a21\u578b\u6240\u9009\u7684\u7ec4\u4ef6\u6570\u91cf\u7528\u4e09\u89d2\u5f62\u7b26\u53f7\u8868\u793a\u3002\u7070\u8272\u7684\u865a\u7ebf\u8868\u793a\u65b9\u5dee\u53c2\u6570\u7684\u767e\u5206\u6bd4\u3002 \u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff08<\/span>showinfo = TRUE<\/span>\uff09\uff0c\u4f1a\u663e\u793a\u5305\u542bPLS\u6a21\u578b\u5185\u90e8\u76f8\u5173\u6027\u7684\u8868\u683c\u3002\u6b64\u5916\uff0c\u9ed8\u8ba4\u7684\u56fe\u5f62\uff08<\/span>showplot = TRUE<\/span>\uff09\u662f\u201cQ2\u56fe\u201d\u548c\u201c\u65b9\u5dee\u89e3\u91ca\u56fe\u201d\uff08\u53c2\u89c1\u56fe7\uff09\uff0c\u5176\u4e2d\u5305\u542b\u6709\u5173<\/span>MultiBaC<\/span>\u6027\u80fd\u7684\u91cd\u8981\u4fe1\u606f\u3002\u201cQ2\u56fe\u201d\u8868\u793aPLS\u6a21\u578b\u9884\u6d4b\u80fd\u529b\u7684Q2\u00b2\u5206\u6570\u3002x\u8f74\u8868\u793a\u63d0\u53d6\u7684PLS\u6a21\u578b\u7684\u7ec4\u4ef6\u6570\uff0cy\u8f74\u4e3aQ2\u00b2\u503c\u3002MultiBaC\u65b9\u6cd5\u7684\u6027\u80fd\u5c06\u968f\u7740Q2\u00b2\u503c\u7684\u589e\u52a0\u800c\u63d0\u9ad8\uff0c\u56e0\u4e3aQ2\u00b2\u503c\u9ad8\u8868\u660ePLS\u5bf9\u7f3a\u5931omics\u7684\u9884\u6d4b\u826f\u597d\uff0c\u56e0\u6b64\u53ef\u4ee5\u66f4\u597d\u5730\u4f30\u8ba1\u6279\u6b21\u6548\u5e94\u3002\u8bf7\u6ce8\u610f\uff0c\u6839\u636e\u77e9\u9635\u7684\u79e9\uff0c\u6bcf\u4e2aPLS\u6a21\u578b\u53ef\u80fd\u5177\u6709\u4e0d\u540c\u7684\u6700\u5927\u7ec4\u4ef6\u6570\u3002\u201c\u65b9\u5dee\u89e3\u91ca\u56fe\u201d\u63d0\u4f9b\u4e86\u4f7f\u7528ARSyN\u65b9\u6cd5\u63d0\u4f9b\u7684ASCA\u5206\u89e3\u89e3\u91ca\u7684\u4e0e\u6279\u6b21\u6548\u5e94\u76f8\u5173\u7684\u53d8\u5f02\u6027\u3002x\u8f74\u8868\u793a\u63d0\u53d6\u7684ASCA\u6a21\u578b\u7684\u7ec4\u4ef6\u6570\uff0cy\u8f74\u53cd\u6620\u4e86\u89e3\u91ca\u65b9\u5dee\u7684\u767e\u5206\u6bd4\u3002\u5728\u8fd9\u79cd\u60c5\u51b5\u4e0b\uff0c\u8f83\u9ad8\u7684\u89e3\u91ca\u65b9\u5dee\u5bfc\u81f4\u66f4\u597d\u7684\u6279\u6b21\u6548\u5e94\u4f30\u8ba1\u3002\u5728\u8fd9\u4e24\u4e2a\u56fe\u4e2d\uff0c\u6bcf\u4e2a\u6a21\u578b\u6240\u9009\u7684\u7ec4\u4ef6\u6570\u7528\u4e09\u89d2\u5f62\u7b26\u53f7\u8868\u793a\u3002\u5728\u201cQ2\u56fe\u201d\u4e2d\uff0c\u6240\u9009\u7684\u7ec4\u4ef6\u6570\u662f\u6700\u5927\u5316Q2\u503c\u7684\u7ec4\u4ef6\u6570\uff0c\u800c\u5728\u201c\u65b9\u5dee\u89e3\u91ca\u56fe\u201d\u4e2d\uff0c\u8fd9\u4e2a\u6570\u5b57\u662f\u6700\u5c0f\u6570\u91cf\u8fbe\u5230\u9ad8\u4e8e\u51fd\u6570<\/span>Variability<\/span>\u53c2\u6570\u7684\u89e3\u91ca\u65b9\u5dee\uff08\u7070\u8272\u7684\u865a\u7ebf\uff09\u7684\u7ec4\u4ef6\u6570\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n\u9010\u6b65\u8fd0\u884cMultiBaC\u6b65\u9aa4<\/strong><\/span><\/p>\nMultiBaC<\/span>\u7684\u6240\u6709\u4e0d\u540c\u6b65\u9aa4\u90fd\u53ef\u4ee5\u4f7f\u7528\u7279\u5b9a\u51fd\u6570\u4ece\u521d\u59cb\u7684<\/span>mbac<\/span>\u5bf9\u8c61\u72ec\u7acb\u8ba1\u7b97\u3002MultiBaC\u7b56\u7565\u53ef\u4ee5\u5206\u4e3a\u4e09\u4e2a\u4e3b\u8981\u6b65\u9aa4\uff0c\u4e0b\u9762\u5c06\u8be6\u7ec6\u63cf\u8ff0\uff1a1) PLS\u6a21\u578b\u62df\u5408\uff0c2) \u7f3a\u5931omics\u7684\u9884\u6d4b\uff0c3)\u6279\u6b21\u6548\u5e94\u4fee\u6b63\u3002 \u4ee5\u4e0b\u662f\u60a8\u8981\u6c42\u7684\u6bb5\u843d\u7684\u7ffb\u8bd1\uff1a<\/span><\/span><\/p>\nPLS\u6a21\u578b\u62df\u5408<\/span><\/p>\ngenModelList\u51fd\u6570\u5728\u4e0d\u540c\u548c\u5e38\u89c1\u7684omic\u6570\u636e\u7c7b\u578b\u4e4b\u95f4\u751f\u6210PLS\u6a21\u578b\uff0c\u5e76\u901a\u8fc7\u4ea4\u53c9\u9a8c\u8bc1\u65b9\u6cd5\u8ba1\u7b97\u6700\u4f73\u7ec4\u4ef6\u6570\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code>my_mbac_2 <- genModelList (my_mbac, test.comp = NULL<\/span>, <\/span><\/code><code> scale = FALSE<\/span>, center = TRUE<\/span>, <\/span><\/code><code> crossval = NULL<\/span>, <\/span><\/code><code> showinfo = TRUE<\/span>) <\/span><\/code><code>## - Model for batch A <\/span><\/span><\/code><code>## - Model for batch B <\/span><\/span><\/code><code>## - Model for batch C<\/span><\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\"><span style=\"font-size: 15px;letter-spacing: 0.034em;text-align: justify;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;font-style: italic;\">genModelList<\/span>\u51fd\u6570\u7684\u53c2\u6570\u4e3a\uff1a<\/span><\/p>\n\u2022<\/span>mbac<\/span>: \u5c5e\u4e8embac\u7c7b\u578b\u5bf9\u8c61\u3002<\/span><\/span><\/p>\n\u2022<\/span>test.comp<\/span>: PLS\u6a21\u578b\u4e2d\u5141\u8bb8\u7684\u6700\u5927\u7ec4\u4ef6\u6570\u3002\u5982\u679c\u4e3aNULL\uff08\u9ed8\u8ba4\u503c\uff09\uff0c\u5219\u4f7f\u7528\u77e9\u9635\u7684\u6700\u5c0f\u6709\u6548\u79e9\u4f5c\u4e3a\u6700\u5927\u7ec4\u4ef6\u6570\u3002<\/span><\/span><\/p>\n\u2022<\/span>scale<\/span>: \u903b\u8f91\u503c\u3002\u662f\u5426\u9700\u8981\u5bf9X\u548cY\u77e9\u9635\u8fdb\u884c\u7f29\u653e\u3002\u9ed8\u8ba4\u503c\u4e3aFALSE\u3002<\/span><\/span><\/p>\n\u2022<\/span>center<\/span>: \u903b\u8f91\u503c\u3002\u662f\u5426\u9700\u8981\u5bf9X\u548cY\u77e9\u9635\u8fdb\u884c\u4e2d\u5fc3\u5316\u3002\u9ed8\u8ba4\u503c\u4e3aTRUE\u3002<\/span><\/span><\/p>\n\u2022<\/span>crossval<\/span>: \u6307\u793a\u4ea4\u53c9\u9a8c\u8bc1\u6bb5\u6570\u7684\u6574\u6570\u3002\u6837\u672c\u6570\uff08\u201cx\u201d\u7684\u884c\u6570\uff09\u5fc5\u987b\u5927\u4e8e\u7b49\u4e8ecrossvalI\u3002\u5982\u679c\u4e3aNULL\uff08\u9ed8\u8ba4\u503c\uff09\uff0c\u5219\u8fdb\u884cleave-one-out\u4ea4\u53c9\u9a8c\u8bc1\u3002<\/span><\/span><\/p>\n\u2022<\/span>showinfo<\/span>: \u903b\u8f91\u503c\uff0c\u6307\u793a\u662f\u5426\u663e\u793a\u51fd\u6570\u8fdb\u5ea6\u4fe1\u606f\u3002\u9ed8\u8ba4\u503c\u4e3aTRUE\u3002 <\/span>genModelList<\/span>\u7684\u8f93\u51fa\u662f\u4e00\u4e2a\u5e26\u6709\u65b0\u69fd<\/span>PLSmodels<\/span>\u7684<\/span>mbac<\/span>\u5bf9\u8c61\uff0c\u8be5\u69fd\u662f\u4f7f\u7528<\/span>ropls<\/span>\u5305\u83b7\u5f97\u7684PLS\u6a21\u578b\u7684\u5217\u8868\u3002\u8f93\u51fa\u7684\u6bcf\u4e2a\u69fd\u5bf9\u5e94\u4e8e<\/span>ListOfBatches<\/span>\u4e2d\u7684\u4e00\u4e2a\u6279\u6b21\u3002\u5982\u679c\u4e00\u4e2a\u6279\u6b21\u5305\u542b\u591a\u4e2a\u975e\u516c\u5171omic\uff0c\u5219<\/span>genModelList<\/span>\u4e2d\u7684\u201c\u6279\u6b21\u201d\u5143\u7d20\u5c06\u4f9d\u6b21\u5305\u542b\u4e0e\u8be5\u6279\u6b21\u4e2d\u7684\u975e\u516c\u5171omic\u6570\u91cf\u76f8\u7b49\u7684\u5143\u7d20\uff0c\u5373\u6bcf\u4e2a\u975e\u516c\u5171omic\u4e00\u4e2aPLS\u6a21\u578b\u3002<\/span> <\/span><o:page><\/o:page><\/p>\n\u7f3a\u5931Omics\u7684\u9884\u6d4b<\/strong><\/span><\/p>\n\u5229\u7528genModelList\u51fd\u6570\u8f93\u51fa\u4e2d\u7684genMissingOmics\u51fd\u6570\uff0c\u5bf9\u521d\u6b65\u7f3a\u5931\u7684Omics\u8fdb\u884c\u9884\u6d4b\u3002<\/span><\/p>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\">multiBatchDesign <- genMissingOmics(my_mbac_2)<\/span><\/p>\n\u8fd0\u884c<\/span>genMissingOmics<\/span>\u51fd\u6570\u540e\u5f97\u5230\u7684\u7ed3\u679c\u662f\u4e00\u4e2aMultiAssayExperiment\u7ed3\u6784\u5217\u8868\u3002\u5728\u8fd9\u79cd\u60c5\u51b5\u4e0b\uff0c\u6bcf\u4e2a\u6279\u6b21\u90fd\u5305\u542bMultiBaC\u4e2d\u5f15\u5165\u7684\u6240\u6709Omics\u3002\u4f8b\u5982\uff0c\u5982\u679c\u6b63\u5728\u7814\u7a76\u4e24\u4e2a\u6279\u6b21\u201cA\u201d\u548c\u201cB\u201d\uff0c\u5176\u4e2d\u201cA\u201d\u5305\u542b\u201cRNA-seq\u201d\u548c\u201cGRO-seq\u201d\u6570\u636e\uff0c\u800c\u201cB\u201d\u5305\u542b\u201cRNA-seq\u201d\u548c\u201cMetabolomics\u201d\u6570\u636e\uff0c\u5219\u5728\u5e94\u7528<\/span>genMissingOmics<\/span>\u51fd\u6570\u540e\uff0c\u6279\u6b21\u201cA\u201d\u5c06\u5305\u542b\u201cRNA-seq\u201d\uff0c\u201cGRO-seq\u201d\u4ee5\u53ca\u9884\u6d4b\u7684\u201cMetabolomics\u201d\u6570\u636e\u3002<\/span><\/span><\/p>\n\u6279\u6b21\u6548\u5e94\u6821\u6b63<\/strong><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"properties\"><code>my_finalwise_mbac<\/span> <- batchCorrection(my_mbac_2, <\/span><\/span><\/code><code> multiBatchDesign<\/span> = multiBatchDesign, <\/span><\/span><\/code><code> Interaction<\/span> = TRUE, <\/span><\/span><\/code><code> Variability<\/span> = 0.90)<\/span><\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\">\u5982\u524d\u6240\u8ff0\uff0cARSyN\u5bf9\u6570\u636e\u77e9\u9635\u8fdb\u884c\u7c7b\u4f3cANOVA\u7684\u5206\u89e3\uff0c\u4ee5\u4f30\u8ba1\u6279\u6b21\u6548\u5e94\uff0c\u7136\u540e\u5728\u6bcf\u4e2a\u5b50\u77e9\u9635\u4e0a\u5e94\u7528PCA\u3002\u6bcf\u4e2aPCA\u7684\u4e3b\u6210\u5206\u6570\u91cf\u901a\u8fc7\u201cVariability\u201d\u53c2\u6570\u8fdb\u884c\u8c03\u6574\u3002\u8be5\u51fd\u6570\u7684\u8f93\u51fa\u7531\u4e24\u4e2a\u4e0d\u540c\u7684\u5bf9\u8c61\u7ec4\u6210\uff1a<\/span><span style=\"font-size: 15px;letter-spacing: 0.034em;text-align: justify;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;font-style: italic;\">CorrectedData<\/span>\u548c<\/span><span style=\"font-size: 15px;letter-spacing: 0.034em;text-align: justify;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;font-style: italic;\">ARSyNmodels<\/span>\u3002\u524d\u8005\u4e0e\u201cListOfBatches\u201d\u69fd\u7684\u7ed3\u6784\u76f8\u540c\u3002\u7136\u800c\uff0c\u5728\u8fd9\u79cd\u60c5\u51b5\u4e0b\uff0c\u6240\u6709\u6279\u6b21\u90fd\u5305\u542bMultiBaC\u4e2d\u5f15\u5165\u7684\u6240\u6709 omics\uff0c\u8fd9\u662f\u901a\u8fc7\u5bf9\u6bcf\u4e2aomics\u6570\u636e\u7c7b\u578b\u5206\u522b\u8fdb\u884c\u6279\u6b21\u6548\u5e94\u6821\u6b63\u540e\u5f97\u5230\u7684\u3002\u8bf7\u6ce8\u610f\uff0c\u6211\u4eec\u4e22\u5f03\u4e86\u9884\u6d4b\u7684omics\u77e9\u9635\uff0c\u53ea\u5728\u540e\u7eed\u7684\u7edf\u8ba1\u5206\u6790\u4e2d\u4f7f\u7528\u7ecf\u8fc7\u6821\u6b63\u7684\u539f\u59cb\u77e9\u9635\u3002<\/span><span style=\"font-size: 15px;letter-spacing: 0.034em;text-align: justify;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;font-style: italic;\">ARSyNmodels<\/span>\u69fd\u5305\u542b\u6bcf\u4e2aomics\u6570\u636e\u7c7b\u578b\u7684ASCA\u5206\u89e3\u6a21\u578b\u3002<\/span><\/p>\nARSyN\u548cMultiBaC\u7ed3\u679c\u7684\u53ef\u89c6\u5316<\/strong> <\/p>\n\u5982\u524d\u6240\u8ff0\uff0c<\/span>ARSyNbac<\/span>\u548c<\/span>MultiBaC<\/span>\u7684\u8f93\u51fa\u662f<\/span>mbac<\/span>\u7c7b\u578b\u7684\u5bf9\u8c61\u3002\u7531\u4e8e<\/span>mbac<\/span>\u7c7b\u5305\u542b\u7ed8\u56fe\u65b9\u6cd5\uff0c\u56e0\u6b64\u53ef\u4ee5\u5c06<\/span>plot\u51fd\u6570\u5e94\u7528\u4e8e<\/span>mbac<\/span>\u5bf9\u8c61\uff0c\u4ee5\u56fe\u5f62\u65b9\u5f0f\u663e\u793a\u6709\u5173\u65b9\u6cd5\u548c\u6570\u636e\u7279\u5f81\u7684\u6027\u80fd\u7684\u9644\u52a0\u4fe1\u606f\u3002<\/span>mbac<\/span>\u5bf9\u8c61\u7684<\/span>plot*\u51fd\u6570\u63a5\u53d7\u51e0\u4e2a\u989d\u5916\u7684\u53c2\u6570\uff1a<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code>plot (x, typeP = \"def\"<\/span>, <\/span><\/code><code> col.by.batch = TRUE<\/span>, <\/span><\/code><code> col.per.group = NULL<\/span>, <\/span><\/code><code> comp2plot = c(1<\/span>,2<\/span>), <\/span><\/code><code> legend.text = NULL<\/span>, <\/span><\/code><code> args.legend = NULL<\/span>, ...)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\"><span style=\"font-family: mp-quote, -apple-system-font, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Hiragino Sans GB", "Microsoft YaHei UI", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 0.034em;text-align: justify;color: rgb(2, 30, 170);font-size: 15px;\">\u63cf\u8ff0\u53c2\u6570\uff1a <\/strong><\/span><span style=\"font-family: mp-quote, -apple-system-font, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Hiragino Sans GB", "Microsoft YaHei UI", "Microsoft YaHei", Arial, sans-serif;letter-spacing: 0.034em;text-align: justify;font-size: 15px;\"> <\/span><\/p>\n\u2022<\/span>x<\/span>: \u7531<\/span>MultiBaC<\/span>\u65b9\u6cd5\u8fd4\u56de\u7684\u201cmbac\u201d\u7c7b\u5bf9\u8c61\u3002<\/span><\/span><\/p>\n\u2022<\/span>typeP<\/span>: \u8981\u663e\u793a\u7684\u56fe\u5f62\u7684\u7c7b\u578b\u3002\u9009\u9879\u6709\uff1a\u201cdef\u201d \uff08\u9ed8\u8ba4\u9009\u9879\uff0c\u5bf9\u4e8eMultiBaC\u662f\u201cQ2 plot\u201d\u548c\u201cExplained variance plot\u201d\uff0c\u5bf9\u4e8eARSyNbac\u8f93\u51fa\u662f\u201cExplained variance plot\u201d\uff09 \u3001\u201cinner\u201d\uff08\u5bf9\u4e8eMultiBaC\u8f93\u51fa\uff0c\u662f\u6bcf\u4e2aPLS\u6a21\u578b\u7684\u5185\u90e8\u76f8\u5173\u6027\u56fe\uff09\u3001\u201cpca.org\u201d\uff08\u5bf9\u4e8eMultiBaC\u6216ARSyNbac\u8f93\u51fa\uff0c\u662f\u539f\u59cb\u6570\u636e\u7684PCA\u56fe\uff09\u3001\u201cpca.cor\u201d\uff08\u5bf9\u4e8eMultiBaC\u6216ARSyNbac\u8f93\u51fa\uff0c\u662f\u4fee\u6b63\u6570\u636e\u7684PCA\u56fe\uff09\u3001\u201cpca.both\u201d\uff08\u5bf9\u4e8eMultiBaC\u6216ARSyNbac\u8f93\u51fa\uff0c\u662f\u539f\u59cb\u548c\u4fee\u6b63\u6570\u636e\u7684PCA\u56fe\uff09\u4ee5\u53ca\u201cbatch\u201d\uff08\u5bf9\u4e8e\u6240\u6709\u8f93\u51fa\uff0c\u662f\u201cBatch effect estimation\u201d\u56fe\uff09\u3002\u8bf7\u6ce8\u610f\uff0c\u5f53\u6240\u6709omics\u5171\u4eab\u76f8\u540c\u7684\u53d8\u91cf\u7a7a\u95f4\u65f6\uff08\u4f8b\u5982\uff0c\u4e3a\u6240\u6709\u6570\u636e\u77e9\u9635\u63d0\u4f9b\u57fa\u56e0\u6807\u8bc6\u7b26\u4f5c\u4e3a\u53d8\u91cf\u540d\uff09\uff0c\u624d\u80fd\u751f\u6210PCA\u56fe\u3002<\/span><\/span><\/p>\n\u2022<\/span>col.by.batch<\/span>: PCA\u56fe\u7684\u53c2\u6570\u3002TRUE\u6216FALSE\u3002\u5982\u679c\u4e3aTRUE\uff08\u9ed8\u8ba4\uff09\uff0c\u5219\u6837\u672c\u6309\u6279\u6b21\u56e0\u7d20\u7740\u8272\u3002\u5982\u679c\u4e3aFALSE\uff0c\u5219\u6837\u672c\u6309\u5b9e\u9a8c\u6761\u4ef6\u7740\u8272\u3002<\/span><\/span><\/p>\n\u2022<\/span>col.per.group<\/span>: PCA\u56fe\u7684\u53c2\u6570\u3002\u6bcf\u4e2a\u7ec4\u7684\u989c\u8272\uff08\u7531\u6279\u6b21\u6216\u5b9e\u9a8c\u6761\u4ef6\u7ed9\u51fa\uff09\u3002\u5982\u679c\u4e3aNULL\uff08\u9ed8\u8ba4\uff09\uff0c\u5219\u989c\u8272\u4ece\u9884\u5b9a\u4e49\u8c03\u8272\u677f\u4e2d\u9009\u53d6\u3002<\/span><\/span><\/p>\n\u2022<\/span>comp2plot<\/span>: PCA\u6216InnerRel\u56fe\u7684\u53c2\u6570\u3002\u6307\u793a\u8981\u7ed8\u5236\u7684\u7ec4\u4ef6\u3002\u9ed8\u8ba4\u662fc(1,2)\uff0c\u8fd9\u610f\u5473\u7740\u5728PCA\u56fe\u4e2d\uff0c\u7b2c1\u4e2a\u7ec4\u4ef6\u7ed8\u5236\u5728\u201cx\u201d\u8f74\u4e0a\uff0c\u7b2c2\u4e2a\u7ec4\u4ef6\u7ed8\u5236\u5728\u201cy\u201d\u8f74\u4e0a\uff0c\u5bf9\u4e8eInnerRel\u56fe\uff0c\u8981\u663e\u793a\u7b2c1\u548c\u7b2c2\u4e2a\u7ec4\u4ef6\u7684\u5185\u90e8\u5173\u7cfb\u56fe\u3002\u5982\u679c\u6307\u793a\u4e86\u591a\u4e2a\u7ec4\u4ef6\uff0c\u5219\u51fd\u6570\u5c06\u8fd4\u56de\u6240\u9700\u6570\u91cf\u7684\u56fe\u4ee5\u663e\u793a\u6240\u6709\u7ec4\u4ef6\u3002<\/span><\/span><\/p>\n\u2022<\/span>legend.text<\/span>: \u7528\u4e8e\u6784\u9020\u56fe\u4f8b\u7684\u6587\u672c\u5411\u91cf\u3002PCA\u56fe\u7684\u53c2\u6570\u3002\u5982\u679c\u4e3aNULL\uff08\u9ed8\u8ba4\uff09\uff0c\u5219\u4f7f\u7528\u5305\u542b\u5728mbac\u5bf9\u8c61\u4e2d\u7684\u6279\u6b21\u6216\u6761\u4ef6\u540d\u79f0\u3002<\/span><\/span><\/p>\n\u2022<\/span>args.legend<\/span>: legend()\u51fd\u6570\u7684\u9644\u52a0\u53c2\u6570\u5217\u8868\uff1b\u5217\u8868\u4e2d\u7684\u540d\u79f0\u7528\u4f5c\u53c2\u6570\u540d\u79f0\u3002\u4ec5\u5728legend.text\u88ab\u63d0\u4f9b\u65f6\u4f7f\u7528\u3002<\/span><\/span><\/p>\n\u2022<\/span>\u2026<\/span>: \u5176\u4ed6\u56fe\u5f62\u53c2\u6570\u3002 \u867d\u7136 <\/span>plot<\/span> \u51fd\u6570\u53ef\u4ee5\u751f\u6210\u4e0a\u8ff0\u6240\u6709\u7c7b\u578b\u7684\u56fe\uff0c\u4f46\u6bcf\u4e2a\u56fe\u4e5f\u53ef\u4ee5\u901a\u8fc7\u5176\u5bf9\u5e94\u7684\u51fd\u6570\u72ec\u7acb\u751f\u6210\uff0c\u8fd9\u4e9b\u51fd\u6570\u5305\u62ec\uff1a<\/span>Q2_plot (mbac)<\/span>\u3001<\/span>explained_varPlot (mbac)<\/span>\u3001<\/span>plot_pca (mbac, typeP = c(\u201cpca.org\u201d, \u201cpca.cor\u201d, \u201cpca.both\u201d), col.by.batch, col.per.group, comp2plot, legend.text, args.legend)<\/span>\u3001<\/span>batchEstPlot (mbac)<\/span>\u4ee5\u53ca <\/span>inner_relPlot (mbac, comp2plot = c(1,2))<\/span>. \u6240\u6709\u8fd9\u4e9b\u56fe\u90fd\u6709\u52a9\u4e8e\u9a8c\u8bc1\u548c\u7406\u89e3<\/span>MultiBaC<\/span>\u6216<\/span>ARSyNbac<\/span>\u7684\u6027\u80fd\u3002\u6240\u6709\u8fd9\u4e9b\u56fe\u90fd\u53ef\u4ee5\u4f7f\u7528<\/span>MultiBaC<\/span>\u7684\u8f93\u51fa\uff0c\u800c\u663e\u793a\u4e0ePLS\u6a21\u578b\u76f8\u5173\u7684\u4fe1\u606f\u56fe\u5219\u4e0d\u9002\u7528\u4e8e<\/span>ARSyNbac<\/span>\u7684\u8f93\u51fa\uff08\u8bf7\u53c2\u89c1<\/span>typeP<\/span>\u53c2\u6570\uff09\u3002 \u9664\u4e86\u201cQ2 plot\u201d\u548c\u201cExplained variance plot\u201d\uff08\u56fe7\uff09\u662f\u9ed8\u8ba4\u7ed8\u5236\u7684\uff0c\u5e76\u4e14\u5728\u524d\u9762\u90e8\u5206\u4ecb\u7ecd\u8fc7\uff0c\u540e\u9762\u90e8\u5206\u7528\u4e8e\u63cf\u8ff0MultiBaC\u5305\u4e2d\u7684\u5176\u4ed6\u56fe\u8868\u3002<\/span> <\/span><o:page><\/o:page><\/p>\nPLS\u6a21\u578b\u4e2d\u7684\u5185\u90e8\u76f8\u5173\u6027<\/strong><\/span><\/p>\n\u5728MultiBaC\u4e2d\u9700\u8981\u9a8c\u8bc1\u7684\u4e00\u4e2a\u91cd\u8981\u65b9\u9762\u662fPLS\u6a21\u578b\u4e2dX\u548cY\u5206\u6570\u4e4b\u95f4\u7684\u5185\u5728\u76f8\u5173\u6027\u3002\u6b63\u5982\u6211\u4eec\u4e4b\u524d\u6307\u51fa\u7684\u90a3\u6837\uff0c\u300aMultiBaC\u300b\u51fd\u6570\u9ed8\u8ba4\u60c5\u51b5\u4e0b\u4ee5\u6570\u503c\u5f62\u5f0f\u663e\u793a\u6b64\u4fe1\u606f\uff0c\u4f46\u4e5f\u53ef\u4ee5\u8c03\u7528\u53ef\u89c6\u5316\u8868\u793a\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code>plot (my_final_mbac, typeP =\"inner\", comp2plot =c(1,2)) <\/span><\/code><code>#<\/span># Hitto see next plot: <\/span><\/span><\/code><code>#<\/span># Inner correlation of scores. Batch: A; Model for omic: GRO <\/span><\/span><\/code><code>#<\/span># Warning in par(initpar): graphical parameter \"cin\" cannot be set<\/span><\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014473\" data-ratio=\"0.5592592592592592\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_IfhW0DTyX0dKkDlOlP5AhJHRGNBicg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVS3QukpNu5XEY3LnU0XRJiaFkRYxIfhW0DTyX0dKkDlOlP5AhJHRGNBicg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"313.20001220703125\" width=\"560.010009765625\" \/><\/span> <\/span>\u56fe8\uff1a<\/span>PLS\u7ec4\u4ef6\u5185\u90e8\u5173\u7cfb\u7684\u7ed8\u56fe<\/span><\/span><\/p>\n\u4ec5\u4ee5\u6279\u6b21\u201cA\u201d\u4e3a\u4f8b\u663e\u793a\u7ed3\u679c\u3002\u6bcf\u4e2a\u9762\u677f\u8868\u793aPCA\u6a21\u578b\u7684\u4e00\u4e2a\u7ec4\u4ef6\u7684\u5185\u90e8\u76f8\u5173\u6027\u3002\u7ea2\u7ebf\u8868\u793a\u5bf9\u89d2\u7ebf\uff0c\u6b64\u65f6\u76f8\u5173\u6027\u6700\u5927\uff081\uff1a1\uff09\u3002 \u5982\u56fe8\u6240\u793a\uff0cPLS\u6a21\u578b\u4e2d\u4e0e\u201cA\u201d\u6279\u6b21\u4e2d\u4e24\u79cd\u7ec4\u5b66\u6570\u636e\u7c7b\u578b\u5747\u76f8\u5173\u7684\u5185\u90e8\u76f8\u5173\u6027\u5f97\u5206\u3002\u867d\u7136\u6211\u4eec\u4ec5\u5c55\u793a\u4e86\u201cA\u201d\u6279\u6b21\u7684\u6563\u70b9\u56fe\uff0c\u4f46\u901a\u8fc7\u8fd0\u884cplot\uff08typeP = \u201cinner\u201d\uff09\u547d\u4ee4\uff0cMultiBaC\u6027\u80fd\u4e2d\u751f\u6210\u7684PLS\u6a21\u578b\u7684\u6240\u6709\u5185\u90e8\u76f8\u5173\u6027\u56fe\u90fd\u5c06\u4ee5\u201cHit to see next plot:\u201d\u6807\u7b7e\u663e\u793a\uff0c\u56e0\u6b64\u9700\u8981\u7528\u6237\u4ea4\u4e92\u624d\u80fd\u663e\u793a\u5b8c\u6574\u7684\u4e00\u7ec4\u56fe\u5f62\u3002\u6a21\u578b\u7684\u76f8\u5173\u4fe1\u606f\uff08\u5305\u62ec\u6279\u6b21\u548c\u7ec4\u5b66\uff09\u4e5f\u4f1a\u5728R\u63d0\u793a\u7b26\u4e2d\u663e\u793a\u3002\u201c\u5185\u90e8\u76f8\u5173\u6027\u56fe\u201d\u662f\u4e00\u4e2a\u5173\u952e\u7ed3\u679c\uff0c\u56e0\u4e3a\u5b83\u4ee3\u8868\u4e86PLS\u6a21\u578b\u7684\u9a8c\u8bc1\u3002\u5728\u6bcf\u4e2a\u6210\u5206\u4e2d\uff0cx\u5206\u6570\uff08t\uff09\u548cy\u5206\u6570\uff08u\uff09\u4e4b\u95f4\u7684\u76f8\u5173\u6027\u5e94\u8be5\u662f\u7ebf\u6027\u7684\uff0c\u5982\u56fe8\u6240\u793a\u3002\u5982\u679c\u89c2\u5bdf\u5230\u975e\u7ebf\u6027\u76f8\u5173\u6027\uff0c\u5219\u9700\u8981\u5bf9\u6570\u636e\u8fdb\u884c\u8f6c\u6362\u3002 <\/span> <\/span><o:page><\/o:page><\/p>\n\u6279\u6b21\u6548\u5e94\u4f30\u8ba1\u56fe<\/strong><\/span><\/p>\n\u6b64\u56fe\u663e\u793a\u4e86\u4f30\u8ba1\u6279\u6b21\u6548\u5e94\u7684\u5e45\u5ea6\u3002\u901a\u5e38\uff0c\u5728\u6267\u884c<\/span>MultiBaC<\/span>\u6216<\/span>ARSyNbac<\/span>\u4e4b\u524d\u4f7f\u7528\u6b64\u56fe\uff0c\u56e0\u4e3a\u5b83\u53ea\u9700\u8981<\/span>createMbac<\/span>\u51fd\u6570\u8fd4\u56de\u7684<\/span>mbac<\/span>\u57fa\u672c\u6570\u636e\u3002<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code>plot<\/span> (my_final_mbac, typeP =\"batch\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\"><\/span><\/span><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014472\" data-ratio=\"0.5824074074074074\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/12_icW8GYkdyuNhJ3aBfh4eKcqwGBoFkg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSKKWd4reLlMWHAQRHKibpp5xsUQicW8GYkdyuNhJ3aBfh4eKcqwGBoFkg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"326.3999938964844\" width=\"560.010009765625\" \/><\/span> <\/span> \u56fe9\uff1a<\/span>\u6279\u6b21\u6548\u5e94\u4f30\u8ba1\u56fe<\/span><\/span><\/p>\n<p style=\"margin-top: 9.0pt;margin-bottom: 9.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\">\u865a\u7ebf\u8868\u793a\u7406\u8bba\u6279\u6b21\u6548\u5e94\u5e45\u5ea6\u3002\u5c0f\u63d0\u7434\u56fe\u8868\u793a\u6570\u636e\u4e2d\u89c2\u5bdf\u5230\u7684\u6279\u6b21\u6548\u5e94\u7cfb\u6570\u7684\u5206\u5e03\u3002 \u9175\u6bcd\u4f8b\u5b50\u7684\u7406\u8bba\u6279\u6b21\u6548\u5e94\u5e45\u5ea6\u5728\u56fe <\/span>9<\/span> \u4e2d\u5c55\u793a\u3002\u5c0f\u63d0\u7434\u56fe\u5c55\u793a\u4e86\u53d8\u91cf\u7a7a\u95f4\u4e2d\u6279\u6b21\u6548\u5e94\u7cfb\u6570\u7684\u5206\u5e03\u60c5\u51b5\uff08\u5bf9\u4e8eRNA-seq\u6570\u636e\u800c\u8a00\uff0c\u8fd9\u4e9b\u53d8\u91cf\u662f\u57fa\u56e0\uff09\u3002\u5177\u6709\u8f83\u9ad8\u503c\u7684\u7cfb\u6570\u5bf9\u5e94\u4e8e\u5bf9\u6279\u6b21\u6548\u5e94\u7684\u5b58\u5728\u8d21\u732e\u6700\u5927\u7684\u90a3\u4e9b\u53d8\u91cf\uff0c\u56e0\u6b64\uff0c\u5f53\u5206\u5e03\u63a5\u8fd1\u96f6\u65f6\uff0c\u6279\u6b21\u6548\u5e94\u8f83\u4f4e\u3002\u5c3d\u7ba1\u5728\u5c0f\u81f3\u4e2d\u7b49\u6279\u6b21\u6548\u5e94\u5e45\u5ea6\u4e0b\uff0cMultiBaC\u7684\u4fee\u6b63\u6027\u80fd\u5df2\u7ecf\u8fc7\u6d4b\u8bd5\u548c\u9a8c\u8bc1\uff0c\u4f46\u5728\u5927\u6279\u91cf\u6548\u5e94\u4e0b\u5176\u6027\u80fd\u6709\u6240\u4e0b\u964d\u3002\u76f8\u6bd4\u4e4b\u4e0b\uff0cARSyN\u53d7\u6279\u6b21\u6548\u5e94\u5e45\u5ea6\u7684\u5f71\u54cd\u5e76\u4e0d\u5927\u3002 \u4ee5\u4e0b\u662fPCA\u56fe\u8868\u7684\u4e2d\u6587\u7ffb\u8bd1\u3002<\/span> <\/span><o:page><\/o:page><\/p>\nPCA\u56fe<\/strong><\/span><\/p>\n\u53ef\u4ee5\u901a\u8fc7\u6bd4\u8f83\u4fee\u6b63\u524d\u540e\u7684PCA\u56fe\u6765\u8bc4\u4f30<\/span>ARSyNbac<\/span>\u6216<\/span>MultiBaC<\/span>\u4fee\u6b63\u7684\u6548\u679c\u3002\u5bf9\u4e8e<\/span>MultiBaC<\/span>\uff0c\u53ea\u6709\u5728\u6240\u6709\u7ec4\u5b66\u6570\u636e\u77e9\u9635\u5171\u4eab\u76f8\u540c\u7684\u53d8\u91cf\u7a7a\u95f4\u65f6\uff0c\u624d\u80fd\u751f\u6210\u8fd9\u79cd\u56fe\u3002\u5728\u6211\u4eec\u63d0\u4f9b\u7684\u9175\u6bcd\u793a\u4f8b\u4e2d\uff0c\u6bcf\u79cd\u7ec4\u5b66\u6570\u636e\u7c7b\u578b\u90fd\u662f\u4ee5\u57fa\u56e0\u76f8\u5173\u4fe1\u606f\u7684\u5f62\u5f0f\u83b7\u5f97\u7684\uff0c\u56e0\u6b64\u53ef\u4ee5\u5c06\u77e9\u9635\u6309\u53d8\u91cf\uff08\u57fa\u56e0\uff09\u5408\u5e76\uff0c\u8fdb\u884cPCA\u5206\u6790\u3002 \u8fd9\u4e9bPCA\u56fe\u5bf9\u4e8e<\/span>ARSyNbac<\/span>\u8f93\u51fa\u7684\u793a\u4f8b\u53ef\u4ee5\u5728ARSyN\u90e8\u5206\u627e\u5230\u3002\u8fd9\u91cc\u6211\u4eec\u6f14\u793a\u4e86\u5982\u4f55\u751f\u6210\u548c\u89e3\u91ca\u5b83\u4eec\u4ee5\u8fdb\u884cMultiBaC\u6821\u6b63\u3002\u5728\u539f\u59cb\u6570\u636e\u4e0a\u7684PCA\uff08\u56fe10\uff1a\u3010\u94fe\u63a5\u3011\uff09\u548c\u6821\u6b63\u6570\u636e\u4e0a\u7684PCA\uff08\u56fe11\uff1a\u3010\u94fe\u63a5\u3011\uff09\u662f\u4f7f\u7528plot\u51fd\u6570\u83b7\u5f97\u7684\uff0c\u5206\u522b\u4f7f\u7528<\/span>\u201ctypeP = pca.org\u201d<\/span>\u6216<\/span>\u201ctypeP = pca.cor\u201d<\/span>\u3002<\/span><\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code>plot<\/span> (my_final_mbac, typeP =\"pca.org\"<\/span>, <\/span><\/code><code> cex.axis =1<\/span>, cex.lab =1<\/span>, cex =3<\/span>, bty =\"L\"<\/span>, <\/span><\/code><code> cex.main =1<\/span>.2<\/span>, pch =19<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\"><\/span><\/span><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014475\" data-ratio=\"0.5555555555555556\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/13_UXNqveDbThx0cwNOdHed6SKvkv1XJA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSCJ07UJYLiaJPjuuXLg51oibQNzUXNqveDbThx0cwNOdHed6SKvkv1XJA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"311.2000427246094\" width=\"560.010009765625\" \/><\/span> <\/span>\u56fe10\uff1a<\/span>\u5728\u539f\u59cb\u6570\u636e\u4e0a\u6267\u884cPCA\u5f97\u5230\u7684\u4e3b\u6210\u5206\u56fe<\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code>plot<\/span> (my_final_mbac, typeP =\"pca.cor\"<\/span>, <\/span><\/code><code> cex.axis =1<\/span>, cex.lab =1<\/span>, cex =3<\/span>, bty =\"L\"<\/span>, <\/span><\/code><code> cex.main =1<\/span>.2<\/span>, pch =19<\/span>) <\/span><\/code><\/pre>\n<\/section>\n<p style=\"mso-style-name: 'Source Code';margin-top: 0.0pt;margin-bottom: 10.0pt;text-align: left;margin-left: 0.0pt;text-indent: 0.0pt;line-height: normal;mso-pagination: widow-orphan;word-break: break-all;font-size: 12.0pt;font-family: Cambria;mso-fareast-font-family: 'Cambria';mso-fareast-language: EN-US;font-weight: normal;mso-bidi-font-weight: normal;\"> <\/span><o:page><\/o:page><\/p>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014474\" data-ratio=\"0.5564814814814815\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/14_OlPLykdqXG3BUknUz5822jP9ibS8WA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSZZaOdq1KlHWv5zjZcb0zoN7ejOlPLykdqXG3BUknUz5822jP9ibS8WA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"311.6000061035156\" width=\"560.010009765625\" \/><\/span> <\/span>\u56fe11\uff1a\u4fee\u6b63\u6570\u636e\u4e0a\u7684\u4e3b\u6210\u5206\u5206\u6790\uff08PCA\uff09\u56fe\uff08\u9ed8\u8ba4\u8bbe\u7f6e)<\/span><\/p>\n\u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff0c\u6b64\u51fd\u6570\u4f7f\u7528\u968f\u673a\u989c\u8272\u8868\u793a\u6bcf\u4e2a\u7ec4\uff08\u9ed8\u8ba4\u60c5\u51b5\u4e0b\u662f\u6279\u6b21\uff09\u3002\u7136\u800c\uff0c\u540c\u65f6\u663e\u793a\u5b9e\u9a8c\u56e0\u7d20\u4fe1\u606f\u4f1a\u5f88\u6709\u7528\u3002\u4e3a\u6b64\uff0c\u6211\u4eec\u5efa\u8bae\u4f7f\u7528\u81ea\u5b9a\u4e49\u7684<\/span>col.per.group<\/span>\u548c<\/span>pch<\/span>\u53c2\u6570\u3002\u56fe<\/span><\/span>12<\/span>\u4e2d\u7ed9\u51fa\u4e86\u4e00\u4e2a\u793a\u4f8b\uff0c\u4f7f\u7528typeP = pca.both\u540c\u65f6\u663e\u793a\u4e24\u4e2aPCA\u56fe\u3002\u6211\u4eec\u8fd8\u53ef\u4ee5\u4f7f\u7528<\/span>comp2plot<\/span>\u53c2\u6570\u7ed8\u5236\u591a\u4e2a\u7ec4\u4ef6\uff0c\u4ee5\u6307\u793a\u6240\u9700\u6570\u91cf\u3002\u7528\u6237\u8fd8\u53ef\u4ee5\u4f7f\u7528\u4e24\u4e2a\u53c2\u6570\u6dfb\u52a0\u81ea\u5b9a\u4e49\u56fe\u4f8b\uff1a<\/span>legend.text<\/span>\u548c<\/span>args.legend<\/span>\u3002\u901a\u8fc7<\/span>legend.text<\/span>\uff0c\u6211\u4eec\u6307\u793a\u56fe\u4f8b\u7684\u6587\u672c\u6807\u7b7e\uff0c\u5176\u4f59\u56fe\u4f8b\u53c2\u6570\u4fdd\u5b58\u5728<\/span>args.legend<\/span>\uff08x\uff0cy\uff0cpch\uff0cfill\uff0ccol\uff0cbty\u7b49)\u4e2d\u3002\u5982\u679c\u5411\u51fd\u6570\u63d0\u4f9b<\/span>legend.text<\/span>\uff0c\u5219\u4e0d\u8003\u8651<\/span>args.legend<\/span>\u3002<\/span><\/span><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code>custom_col <-c(\"brown2\"<\/span>, \"dodgerblue\"<\/span>, \"forestgreen\"<\/span>) <\/span><\/code><code>custom_pch <-c(19<\/span>,19<\/span>,19<\/span>,1<\/span>,1<\/span>,1<\/span>,15<\/span>,15<\/span>,15<\/span>,0<\/span>,0<\/span>,0<\/span>, # batch A <\/span><\/span><\/code><code> 19<\/span>,19<\/span>,1<\/span>,1<\/span>,17<\/span>,17<\/span>,2<\/span>,2<\/span>, # batch B <\/span><\/span><\/code><code> 19<\/span>,19<\/span>,1<\/span>,1<\/span>,18<\/span>,18<\/span>,5<\/span>,5<\/span>) # batch C <\/span><\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>plot(my_final_mbac, typeP =\"pca.both\"<\/span>, col.by.batch =TRUE<\/span>, <\/span><\/code><code> col.per.group = custom_col, comp2plot =1<\/span>:3<\/span>, <\/span><\/code><code> cex.axis =1.3<\/span>, cex.lab =1.2<\/span>, cex =3<\/span>, bty =\"L\"<\/span>, <\/span><\/code><code> cex.main =1.7<\/span>, pch = custom_pch, <\/span><\/code><code> legend.text =c(\"Color\"<\/span>, names(my_final_mbac$ListOfBatches), <\/span><\/code><code> \"Shape\"<\/span>, c(\"RNA\"<\/span>, \"GRO\"<\/span>, \"RIBO\"<\/span>, \"PAR\"<\/span>), <\/span><\/code><code> \"Fill\"<\/span>, levels(colData(my_final_mbac$ListOfBatches$A)$tfactor)), <\/span><\/code><code> args.legend =list<\/span>(\"x\"<\/span>=\"topright\"<\/span>, <\/span><\/code><code> \"pch\"<\/span>=c(NA, 15<\/span>, 15<\/span>, 15<\/span>, <\/span><\/code><code> NA, 19<\/span>, 15<\/span>, 17<\/span>, 18<\/span>, <\/span><\/code><code> NA, 19<\/span>, 1<\/span>), <\/span><\/code><code> \"col\"<\/span>=c(NA, \"brown2\"<\/span>, \"dodgerblue\"<\/span>, \"forestgreen\"<\/span>, <\/span><\/code><code> NA, rep(1<\/span>, 4<\/span>), <\/span><\/code><code> NA, 1<\/span>, 1<\/span>), <\/span><\/code><code> \"bty\"<\/span>=\"n\"<\/span>, <\/span><\/code><code> \"cex\"<\/span>=2<\/span>)) <\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014476\" data-ratio=\"0.7888888888888889\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/15_AwWHqpCqekDhpGrzITvdXsNbwRjpdw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwaOtnqQlN0kicqNFL8Q1tVSVew362JosFQgq2EWer01n6qAAwWHqpCqekDhpGrzITvdXsNbwRjpdw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"442.0099792480469\" width=\"560.010009765625\" \/><\/span> <\/span>\u56fe12\uff1a<\/span>\u5b9a\u5236\u7684\u4e3b\u6210\u5206\u5206\u6790\u56fe<\/span><\/span><\/p>\n\u539f\u59cb\u6570\u636e\uff08\u5de6\u4fa7\u9762\u677f\uff09\u548c\u4fee\u6b63\u6570\u636e\uff08\u53f3\u4fa7\u9762\u677f\uff09\u3002\u4e0a\u56fe\u663e\u793a\u7b2c\u4e8c\u4e3b\u6210\u5206\uff08PC\uff09\u4e0e\u7b2c\u4e00\u4e3b\u6210\u5206\u7684\u5173\u7cfb\uff0c\u800c\u4e0b\u56fe\u5219\u663e\u793a\u7b2c\u4e09\u4e3b\u6210\u5206\u4e0e\u7b2c\u4e00\u4e3b\u6210\u5206\u7684\u5173\u7cfb\u3002 \u5728\u8fd9\u79cd\u60c5\u51b5\u4e0b\uff0c\u6279\u6b21\u6548\u5e94\u6821\u6b63\u53ef\u5728\u901a\u7528\u6570\u636e\uff08RNA-seq\u3001\u70b9\uff09\u4e2d\u89c2\u5bdf\u5230\u3002\u5f53\u901a\u7528\u6570\u636e\u653e\u5728\u4e00\u8d77\u540e\uff0c\u6279\u6b21\u6548\u5e94\u5df2\u88ab\u79fb\u9664\uff0c\u5e76\u4e14\u5728\u6821\u6b63\u540e\uff0c\u8fd9\u4e9b\u6210\u5206\uff08\u5c24\u5176\u662f\u7b2c\u4e8c\u548c\u7b2c\u4e09\u6210\u5206)\u4f1a\u6839\u636e\u5b9e\u9a8c\u6761\u4ef6\u5bf9\u901a\u7528\u6570\u636e\u8fdb\u884c\u5206\u79bb\uff0c\u800c\u4e0d\u662f\u6839\u636e\u6279\u6b21\u8fdb\u884c\u5206\u79bb\u3002\u5982\u56fe\u4f8b\u6240\u793a\uff0c\u70b9\u7684\u5f62\u72b6\u8868\u793a omic\u6570\u636e\u7c7b\u578b\uff0c\u7136\u800c\u6279\u6b21\u6548\u5e94\u6821\u6b63\u4ec5\u5728\u901a\u7528\u6570\u636e\u4e2d\u53ef\u89c1\u3002<\/span><\/span><\/p>\n\u603b\u7ed3<\/strong><\/span><\/p>\nMultiBaC\u662f\u7528\u4e8e\u591a\u7ec4\u5b66\u548c\u9690\u85cf\u6279\u6b21\u6548\u5e94\u573a\u666f\u4e2d\u7684\u6279\u91cf\u6548\u5e94\u53bb\u9664\u5de5\u5177\u3002\u8be5\u5305\u63d0\u4f9b\u591a\u79cd\u56fe\u5f62\u8f93\u51fa\uff0c\u7528\u4e8e\u6a21\u578b\u9a8c\u8bc1\u548c\u6279\u91cf\u6548\u5e94\u6821\u6b63\u8bc4\u4f30\u3002\u5feb\u548c\u5c0f\u679c\u4e00\u8d77\u7528MultiBaC R\u5305\u66f4\u6709\u6548\u5730\u5904\u7406\u591a\u7ec4\u5b66\u5b9e\u9a8c\u4e2d\u7684\u6279\u91cf\u6548\u5e94\u95ee\u9898\uff0c\u4ece\u800c\u63d0\u9ad8\u6570\u636e\u5206\u6790\u7684\u51c6\u786e\u6027\u548c\u53ef\u9760\u6027\u5427\uff01<\/span> <\/span><o:page><\/o:page><\/p>\n\u53c2\u8003\u6587\u732e<\/strong><\/span><\/p>\n1.Nueda MJ, Ferrer A, Conesa A. ARSyN: A method for the identification and removal of systematic noise in multifactorial time course microarray experiments. Biostatistics. 2012;13:553\u201366.<\/span><\/p>\n2.Pelechano V, P\u00e9rez-Ort\u00edn JE. There is a steady-state transcriptome in exponentially growing yeast cells. Yeast. 2010;27:413\u201322. doi:<\/span>10.1002\/yea.1768<\/span>.<\/span><\/p>\n3.Garc\u00eda-Mart\u00ednez J, Aranda A, P\u00e9rez-Ort\u00edn J. Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Molecular Cell. 15:303\u201313. doi:<\/span>10.1016\/j.molcel.2004.06.004<\/span>.<\/span><\/p>\n4.Pelechano V, Ch\u00e1vez S, P\u00e9rez-Ort\u00edn JE. A complete set of nascent transcription rates for yeast genes. PloS one. 5:e15442; e15442\u20132. doi:<\/span>10.1371\/journal.pone.0015442<\/span>.<\/span><\/p>\n5.Zid BM, O\u2019Shea EK. Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast. Nature. 514:117\u201321. doi:<\/span>10.1038\/nature13578<\/span>.<\/span><\/p>\n6.Freeberg MA, Han T, Moresco JJ, Kong A, Yang Y-C, Lu ZJ, et al. Pervasive and dynamic protein binding sites of the mRNA transcriptome in saccharomyces cerevisiae. Genome biology. 14:R13\u20133. doi:<\/span>10.1186\/gb-2013-14-2-r13<\/span>.<\/span><\/p>\n<section powered-by=\"xiumi.us\" style=\"margin-bottom: 0px;\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100014478\" data-ratio=\"0.5555555555555556\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/16_VmRkv7tSNKliafDnsuFR7BoeDgBrww.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAxPqeNQsFjm2HibIuSld9Nh9GicQSWhJwHjia5tEevQvDIebLErVmRkv7tSNKliafDnsuFR7BoeDgBrww\/640?wx_fmt=jpeg&from=appmsg'\" data-type=\"jpeg\" data-w=\"900\" style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\" \/> <\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"margin-top: 0pt;margin-bottom: 0pt;margin-left: 0pt;letter-spacing: 0.578px;text-indent: 0pt;text-wrap: wrap;text-align: justify;line-height: normal;font-size: 12pt;font-family: helvetica;color: rgb(0, 0, 0);break-after: auto;\"><\/span><\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;color: rgba(0, 0, 0, 0.9);font-family: mp-quote, -apple-system-font, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Hiragino Sans GB", "Microsoft YaHei UI", "Microsoft YaHei", Arial, sans-serif;text-align: justify;\"><\/span><img decoding=\"async\" class=\"rich_pages wxw-img\" data-imgfileid=\"100014477\" data-ratio=\"0.38981481481481484\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/17_FbEg9fibwQicL8l2ExKOZZTmAHXabQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAx3HetBkB7aOGibFWKqibqIATyC4zFibzCgdrxFwRep6cDMLIbA0FbEg9fibwQicL8l2ExKOZZTmAHXabQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;caret-color: rgba(0, 0, 0, 0);\" \/><\/span><\/p>\n<section powered-by=\"xiumi.us\" style=\"margin-bottom: 0px;letter-spacing: 0.578px;text-wrap: wrap;outline: 0px;font-family: system-ui, -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Hiragino Sans GB", "Microsoft YaHei UI", "Microsoft YaHei", Arial, sans-serif;background-color: rgb(255, 255, 255);text-align: left;\">\n<section style=\"outline: 0px;font-size: 16px;\">\n<section powered-by=\"xiumi.us\" style=\"margin: 10px;outline: 0px;justify-content: flex-start;display: flex;flex-flow: row;\">\n<section style=\"padding-right: 10px;padding-left: 10px;outline: 0px;display: inline-block;width: 558px;vertical-align: top;border-style: dashed;border-width: 1px;border-color: rgb(62, 62, 62);align-self: flex-start;flex: 0 0 auto;\">\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 10px;outline: 0px;\">\n<section style=\"outline: 0px;display: inline-block;width: 536px;border-width: 0px 0px 0px 10px;border-style: solid;border-left-color: rgb(144, 215, 236);border-right-color: rgb(46, 172, 109);box-shadow: rgb(0, 0, 0) 0px 0px 0px;border-bottom-left-radius: 0px;\">\n<section powered-by=\"xiumi.us\" style=\"padding-right: 3px;padding-left: 3px;outline: 0px;\">\n<section style=\"margin-top: 0.95em;margin-bottom: -0.65em;outline: 0px;display: inline-block;width: 520px;vertical-align: top;\">\n<section style=\"margin-top: -1em;padding: 3px 10px;outline: 0px;display: inline-block;vertical-align: top;color: rgb(0, 154, 68);\">\n\u5f80\u671f\u63a8\u8350<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"outline: 0px;text-align: justify;\">\n<section style=\"outline: 0px;letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491794&idx=1&sn=2b7a4de95169c79202e44813885a8250&chksm=cf7f7017f808f9015689839fe4057fd418bf7b20eb1dfb5a28cd92e56a41b5605e62bfbc16fb&scene=21#wechat_redirect\" textvalue=\"1.\u642d\u5efa\u751f\u4fe1\u5206\u6790\u6d41\u6c34\u7ebf\uff0c\u5982\u5de5\u5382\u4e00\u683724\u5c0f\u65f6\u8fd0\u8f6cSnakemake\u2014\u2014\u8fdb\u9636\u547d\u4ee4\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" hasload=\"1\" style=\"color: var(--weui-LINK);outline: 0px;cursor: pointer;font-size: 14px;\" rel=\"noopener\">1.\u642d\u5efa\u751f\u4fe1\u5206\u6790\u6d41\u6c34\u7ebf\uff0c\u5982\u5de5\u5382\u4e00\u683724\u5c0f\u65f6\u8fd0\u8f6cSnakemake\u2014\u2014\u8fdb\u9636\u547d\u4ee4<\/a> <\/section>\n<section style=\"outline: 0px;letter-spacing: 0.578px;line-height: 1.75em;\"><a 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