{"id":27736,"date":"2024-02-02T16:24:31","date_gmt":"2024-02-02T08:24:31","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=27736"},"modified":"2024-02-02T16:24:32","modified_gmt":"2024-02-02T08:24:32","slug":"multibac%ef%bc%9a%e5%8e%bb%e9%99%a4%e5%a4%9a%e7%bb%84%e5%ad%a6%e6%95%b0%e6%8d%ae%e6%89%b9%e6%ac%a1%e6%95%88%e5%ba%94","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=27736","title":{"rendered":"MultiBaC\uff1a\u53bb\u9664\u591a\u7ec4\u5b66\u6570\u636e\u6279\u6b21\u6548\u5e94"},"content":{"rendered":"<p>\u5728\u751f\u7269\u4fe1\u606f\u5b66\u9886\u57df\uff0c\u968f\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<\/p>\n<p>\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<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"185\" class=\"wp-image-27737\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-12.png?resize=640%2C185\" alt=\"fig:\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-12.png?w=1872 1872w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-12.png?resize=300%2C87 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-12.png?resize=1024%2C295 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-12.png?resize=768%2C222 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-12.png?resize=1536%2C443 1536w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-12.png?resize=600%2C173 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-12.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p><a href=\"#post-27736-multibac\u53bb\u9664\u591a\u7ec4\u5b66\u6570\u636e\u6279\u6b21\u6548\u5e94\">MultiBaC\uff1a\u53bb\u9664\u591a\u7ec4\u5b66\u6570\u636e\u6279\u6b21\u6548\u5e94<\/a><br \/>\n<a href=\"#post-27736-\u7b80\u4ecb\">\u7b80\u4ecb<\/a><br \/>\n<a href=\"#post-27736-\u5355\u4e2a\u7ec4\u5b66\u6570\u636e\u6279\u6b21\u6548\u5e94\u7684\u4fee\u6b63\">\u5355\u4e2a\u7ec4\u5b66\u6570\u636e\u6279\u6b21\u6548\u5e94\u7684\u4fee\u6b63<\/a><br \/>\n<a href=\"#post-27736-\u5173\u4e8earsyn\">\u5173\u4e8eARSyN<\/a><br \/>\n<a href=\"#post-27736-arsyn\u65b9\u6cd5\u6982\u8ff0\">ARSyN\u65b9\u6cd5\u6982\u8ff0<\/a><br \/>\n<a href=\"#post-27736-\u793a\u4f8b\u9175\u6bcd\u8868\u8fbe\u6570\u636e\">\u793a\u4f8b\uff1a\u9175\u6bcd\u8868\u8fbe\u6570\u636e<\/a><br \/>\n<a href=\"#post-27736-arsynbac\u8f93\u5165\u6570\u636e\">ARSyNbac\u8f93\u5165\u6570\u636e<\/a><br \/>\n<a href=\"#post-27736-arsynbac\u6821\u6b63\">ARSyNbac\u6821\u6b63<\/a><br \/>\n<a href=\"#post-27736-arsynbac\u6279\u91cf\u6548\u5e94\u6821\u6b63\">ARSyNbac\u6279\u91cf\u6548\u5e94\u6821\u6b63<\/a><br \/>\n<a href=\"#post-27736-arsynbac\u53bb\u566a\">ARSyNbac\u53bb\u566a<\/a><br \/>\n<a href=\"#post-27736-arsynbac\u4e24\u79cd\u6a21\u5f0f\">ARSyNbac\u4e24\u79cd\u6a21\u5f0f<\/a><br \/>\n<a href=\"#post-27736-\u591a\u7ec4\u5b66\u6570\u636e\u96c6\u4e0a\u7684\u6279\u6b21\u6548\u5e94\u6821\u6b63\">\u591a\u7ec4\u5b66\u6570\u636e\u96c6\u4e0a\u7684\u6279\u6b21\u6548\u5e94\u6821\u6b63<\/a><br \/>\n<a href=\"#post-27736-\u5173\u4e8emultibac\">\u5173\u4e8eMultiBaC<\/a><br \/>\n<a href=\"#post-27736-multibac-\u65b9\u6cd5\u6982\u8ff0\">MultiBaC \u65b9\u6cd5\u6982\u8ff0<\/a><br \/>\n<a href=\"#post-27736-\u793a\u4f8b\u9175\u6bcd\u591a\u7ec4\u5b66\u6570\u636e\u96c6\">\u793a\u4f8b\uff1a\u9175\u6bcd\u591a\u7ec4\u5b66\u6570\u636e\u96c6<\/a><br \/>\n<a href=\"#post-27736-multibac\u8f93\u5165\u6570\u636e\">MultiBaC\u8f93\u5165\u6570\u636e<\/a><br \/>\n<a href=\"#post-27736-multibac-correction\">MultiBaC correction<\/a><br \/>\n<a href=\"#post-27736-\u9010\u6b65\u8fd0\u884cmultibac\u6b65\u9aa4\">\u9010\u6b65\u8fd0\u884cMultiBaC\u6b65\u9aa4<\/a><br \/>\n<a href=\"#post-27736-pls\u6a21\u578b\u62df\u5408\">PLS\u6a21\u578b\u62df\u5408<\/a><br \/>\n<a href=\"#post-27736-\u7f3a\u5931omics\u7684\u9884\u6d4b\">\u7f3a\u5931Omics\u7684\u9884\u6d4b<\/a><br \/>\n<a href=\"#post-27736-\u6279\u6b21\u6548\u5e94\u6821\u6b63\">\u6279\u6b21\u6548\u5e94\u6821\u6b63<\/a><br \/>\n<a href=\"#post-27736-arsyn\u548cmultibac\u7ed3\u679c\u7684\u53ef\u89c6\u5316\">ARSyN\u548cMultiBaC\u7ed3\u679c\u7684\u53ef\u89c6\u5316<\/a><br \/>\n<a href=\"#post-27736-pls\u6a21\u578b\u4e2d\u7684\u5185\u90e8\u76f8\u5173\u6027\">PLS\u6a21\u578b\u4e2d\u7684\u5185\u90e8\u76f8\u5173\u6027<\/a><br \/>\n<a href=\"#post-27736-\u6279\u6b21\u6548\u5e94\u4f30\u8ba1\u56fe\">\u6279\u6b21\u6548\u5e94\u4f30\u8ba1\u56fe<\/a><br \/>\n<a href=\"#post-27736-pca\u56fe\">PCA\u56fe<\/a><br \/>\n<a href=\"#post-27736-\u603b\u7ed3\">\u603b\u7ed3<\/a><br \/>\n<a href=\"#post-27736-\u53c2\u8003\u6587\u732e\">\u53c2\u8003\u6587\u732e<\/a><\/p>\n<h2>\u7b80\u4ecb<\/h2>\n<p>\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<br \/>\n\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 [<a href=\"https:\/\/www.bioconductor.org\/packages\/release\/bioc\/vignettes\/MultiBaC\/inst\/doc\/MultiBaC.html#ref-Nueda2012\">1<\/a>]\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<br \/>\nBECAs\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<br \/>\n<strong>MultiBaC<\/strong>\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<\/p>\n<h2>\u5355\u4e2a\u7ec4\u5b66\u6570\u636e\u6279\u6b21\u6548\u5e94\u7684\u4fee\u6b63<\/h2>\n<h3>\u5173\u4e8eARSyN<\/h3>\n<h3>ARSyN\u65b9\u6cd5\u6982\u8ff0<\/h3>\n<p>ARSyN\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<a href=\"https:\/\/www.bioconductor.org\/packages\/release\/bioc\/vignettes\/MultiBaC\/inst\/doc\/MultiBaC.html#ref-Nueda2012\">1<\/a>\uff09\u3002\u5728<strong>MultiBaC<\/strong>\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<br \/>\n\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<br \/>\n\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<\/p>\n<h3>\u793a\u4f8b\uff1a\u9175\u6bcd\u8868\u8fbe\u6570\u636e<\/h3>\n<p>\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[<a href=\"https:\/\/www.bioconductor.org\/packages\/release\/bioc\/vignettes\/MultiBaC\/inst\/doc\/MultiBaC.html#ref-JE1\">2<\/a>]; Lab B\u662f\u54c8\u4f5b\u5927\u5b66\u7684\u5206\u5b50\u548c\u7ec6\u80de\u751f\u7269\u5b66\u90e8\u95e8\uff08\u5b58\u53d6\u53f7GSE56622\uff09[<a href=\"https:\/\/www.bioconductor.org\/packages\/release\/bioc\/vignettes\/MultiBaC\/inst\/doc\/MultiBaC.html#ref-RIBO\">5<\/a>]; \u548cLab C\u662f\u7ea6\u7ff0\u970d\u666e\u91d1\u65af\u5927\u5b66\u7684\u751f\u7269\u5b66\u90e8\u95e8\uff08\u5b58\u53d6\u53f7GSE43747\uff09[<a href=\"https:\/\/www.bioconductor.org\/packages\/release\/bioc\/vignettes\/MultiBaC\/inst\/doc\/MultiBaC.html#ref-PARCLIP\">6<\/a>]\u3002<br \/>\n\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<em>MutiBaC<\/em>\u5305\u4e2d\uff0c\u7528\u4e8e\u8bf4\u660e\u8be5\u5305\u7684\u7528\u6cd5\u3002\u53ef\u4ee5\u4f7f\u7528<em>data(\u201cmultiyeast\u201d\uff09<\/em>\u6307\u4ee4\u52a0\u8f7d\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u3002<br \/>\n\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<br \/>\n<img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"358\" class=\"wp-image-27738\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-13.png?resize=640%2C358\" alt=\"fig:\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-13.png?w=1175 1175w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-13.png?resize=300%2C168 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-13.png?resize=1024%2C573 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-13.png?resize=768%2C430 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-13.png?resize=600%2C336 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><br \/>\n\u56fe1\uff1a<strong>\u539f\u59cb\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684\u4e3b\u6210\u5206\u5206\u6790\u56fe\uff08\u6821\u6b63\u524d\uff09<\/strong>\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<\/p>\n<h3>ARSyNbac\u8f93\u5165\u6570\u636e<\/h3>\n<p><strong>MultiBaC<\/strong>\u5305\u4f7f\u7528\u7684\u662f<em>MultiAssayExperiment<\/em>\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<em>data.frame<\/em>\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<em>createMbac<\/em>\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<\/p>\n<p>data(&#8220;multiyeast&#8221;)<br \/>\nhead(A.rna)<br \/>\n## A.rna_Glu+_1 A.rna_Glu+_2 A.rna_Glu+_3 A.rna_Glu-_1 A.rna_Glu-_2<br \/>\n## YOR324C 7.174264 6.976815 7.482661 8.020596 7.736636<br \/>\n## YGL104C 4.239493 4.284775 3.100898 4.957403 3.673252<br \/>\n## YOR142W 8.819824 8.496966 9.026971 10.374525 10.294006<br \/>\n## YOR052C 6.721211 7.011932 7.557519 8.504503 8.586738<br \/>\n## YGR038W 5.878483 5.894121 6.468361 7.856822 7.806318<br \/>\n## YER087W 5.131089 5.295029 5.750657 2.920250 5.496136<br \/>\n## A.rna_Glu-_3<br \/>\n## YOR324C 7.922425<br \/>\n## YGL104C 1.587184<br \/>\n## YOR142W 10.979224<br \/>\n## YOR052C 8.221168<br \/>\n## YGR038W 8.108436<br \/>\n## YER087W 2.879254<\/p>\n<p>\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<\/p>\n<p>data_RNA&lt;- createMbac (inputOmics = list(A.rna, B.rna, C.rna),<br \/>\nbatchFactor = c(&#8220;A&#8221;, &#8220;B&#8221;, &#8220;C&#8221;),<br \/>\nexperimentalDesign = list(&#8220;A&#8221; = c(&#8220;Glu+&#8221;, &#8220;Glu+&#8221;,<br \/>\n&#8220;Glu+&#8221;, &#8220;Glu-&#8220;,<br \/>\n&#8220;Glu-&#8220;, &#8220;Glu-&#8220;),<br \/>\n&#8220;B&#8221; = c(&#8220;Glu+&#8221;, &#8220;Glu+&#8221;,<br \/>\n&#8220;Glu-&#8220;, &#8220;Glu-&#8220;),<br \/>\n&#8220;C&#8221; = c(&#8220;Glu+&#8221;, &#8220;Glu+&#8221;,<br \/>\n&#8220;Glu-&#8220;, &#8220;Glu-&#8220;)),<br \/>\nomicNames = &#8220;RNA&#8221;)<\/p>\n<p>\u4ee5\u4e0b\u662f<em>createMbac<\/em>\u51fd\u6570\u53c2\u6570\u7684\u8bf4\u660e\uff1a<\/p>\n<ul>\n<li><strong>inputOmics<\/strong> \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<\/li>\n<li><strong>batchFactor<\/strong> \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<\/li>\n<li><strong>experimentalDesign<\/strong> \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 <em>batches<\/em> \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 <em>batches<\/em> \u53c2\u6570\u4e2d\u7684\u540d\u79f0\u76f8\u540c\u5e76\u6309\u76f8\u540c\u987a\u5e8f\u6392\u5217\u3002<\/li>\n<li><strong>omicNames<\/strong> \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<\/li>\n<li><strong>commonOmic<\/strong> \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<br \/>\n\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<\/li>\n<li><strong>ListOfBatches<\/strong>: \u4e00\u4e2a\u5305\u542b\u591a\u4e2aMultiAssayExperiment\u5bf9\u8c61\u7684\u5217\u8868\uff08\u6bcf\u4e2a\u6279\u6b21\u4e00\u4e2a\u5bf9\u8c61\uff09\u3002<\/li>\n<li><strong>CorrectedData<\/strong>: \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<\/li>\n<li><strong>PLSmodels<\/strong>: \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<\/li>\n<li><strong>ARSyNmodels<\/strong>: \u7531ARSyNbac\u6216MultiBaC\u51fd\u6570\u521b\u5efa\u7684ARSyN\u6a21\u578b\u3002<\/li>\n<li><strong>InnerRelation<\/strong>: \u4e00\u4e2a\u7c7b\u4e3a<em>data.frame<\/em>\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<\/li>\n<li><strong>commonOmic<\/strong>: \u6279\u6b21\u95f4\u516c\u5171omic\u7684\u540d\u79f0\u3002<br \/>\n\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<\/li>\n<\/ul>\n<p>summary(data_RNA)<br \/>\n## [1] &#8220;Object of class mbac: It contains 3 different bacthes and 1 omic type(s).&#8221;<\/p>\n<table>\n<thead>\n<tr>\n<th><\/th>\n<th>RNA<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td>A<\/td>\n<td>True<\/td>\n<\/tr>\n<tr>\n<td>B<\/td>\n<td>True<\/td>\n<\/tr>\n<tr>\n<td>C<\/td>\n<td>True<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h3>ARSyNbac\u6821\u6b63<\/h3>\n<p><strong>MultiBaC<\/strong>\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<em>ARSyNbac<\/em>\u51fd\u6570\uff0c\u5b83\u5141\u8bb8\u4ee5\u4e0b\u53c2\u6570\uff1a<\/p>\n<p>ARSyNbac (mbac, batchEstimation = TRUE, filterNoise = TRUE,<br \/>\nInteraction=FALSE, Variability = 0.90, beta = 2,<br \/>\nmodelName = &#8220;Model 1&#8221;,<br \/>\nshowplot = TRUE)<\/p>\n<ul>\n<li><strong>mbac<\/strong>: \u901a\u8fc7 <em>createMbac<\/em> \u751f\u6210\u7684 mbac \u5bf9\u8c61\u3002<\/li>\n<li><strong>batchEstimation<\/strong>: \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<\/li>\n<li><strong>filterNoise<\/strong>: \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<\/li>\n<li><strong>Interaction<\/strong>: \u903b\u8f91\u503c\u3002\u662f\u5426\u5efa\u7acb\u56e0\u7d20\u4e4b\u95f4\u7684\u4ea4\u4e92\u6a21\u578b\uff08\u9ed8\u8ba4\u4e3a FALSE\uff09\u3002<\/li>\n<li><strong>Variability<\/strong>: \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<\/li>\n<li><strong>beta<\/strong>: \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<\/li>\n<li><strong>modelName<\/strong>: \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<\/li>\n<li><strong>showplot<\/strong>: \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<br \/>\n\u56e0\u6b64\uff0cARSyNbac\u51fd\u6570\u63d0\u4f9b\u4e86\u4e09\u79cd\u5206\u6790\u7c7b\u578b\uff1a\u5f53\u63d0\u4f9b\u6279\u6b21\u4fe1\u606f\u65f6\u8fdb\u884c<strong>ARSyNbac\u6279\u6b21\u6548\u5e94\u6821\u6b63<\/strong>\uff0c\u5f53\u6279\u6b21\u4fe1\u606f\u672a\u77e5\u65f6\u8fdb\u884c<strong>ARSyNbac\u566a\u58f0\u6291\u5236<\/strong>\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<\/li>\n<\/ul>\n<h4>ARSyNbac\u6279\u91cf\u6548\u5e94\u6821\u6b63<\/h4>\n<p>\u5f53\u5728<em>mbac<\/em>\u8f93\u5165\u5bf9\u8c61\u7684<em>batchFactor<\/em>\u53c2\u6570\u4e2d\u6307\u5b9a\u6279\u6b21\u65f6\uff0c\u53ef\u4ee5\u901a\u8fc7\u9009\u62e9<em>batchEstimation = TRUE<\/em>\uff08\u4ec5\u8003\u8651\u4e00\u4e2a\u6279\u6b21\u6548\u5e94\u6e90\uff0c<em>filterNoise = FALSE<\/em>\uff09\u6765\u4f30\u8ba1\u5e76\u6d88\u9664\u5176\u5f71\u54cd\u3002\u6b64\u5916\uff0c\u901a\u8fc7\u8bbe\u7f6e<em>Interaction=TRUE<\/em>\u53ef\u4ee5\u7814\u7a76\u5b9e\u9a8c\u56e0\u7d20\u4e0e\u6279\u6b21\u56e0\u7d20\u4e4b\u95f4\u7684\u76f8\u4e92\u4f5c\u7528\u3002<\/p>\n<p>par(mfrow = c(1,2))<br \/>\narsyn_1 &lt;- ARSyNbac(data_RNA, modelName = &#8220;RNA&#8221;, Variability = 0.95,<br \/>\nbatchEstimation = TRUE, filterNoise = FALSE, Interaction = FALSE)<br \/>\nplot(arsyn_1, typeP=&#8221;pca.cor&#8221;, bty = &#8220;L&#8221;,<br \/>\npch = custom_pch, cex = 3, col.per.group = custom_col,<br \/>\nlegend.text = c(&#8220;Color: Batch&#8221;, names(data_RNA$ListOfBatches),<br \/>\n&#8220;Fill: Cond.&#8221;, unique(colData(data_RNA$ListOfBatches$A)$tfactor)),<br \/>\nargs.legend = list(&#8220;x&#8221; = &#8220;topright&#8221;,<br \/>\n&#8220;pch&#8221; = c(NA, 15, 15, 15,<br \/>\nNA, 15, 0),<br \/>\n&#8220;col&#8221; = c(NA, &#8220;brown2&#8221;, &#8220;dodgerblue&#8221;, &#8220;forestgreen&#8221;,<br \/>\nNA, 1, 1),<br \/>\n&#8220;bty&#8221; = &#8220;n&#8221;,<br \/>\n&#8220;cex&#8221; = 1.2))<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"357\" class=\"wp-image-27739\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-14.png?resize=640%2C357\" alt=\"fig:\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-14.png?w=1400 1400w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-14.png?resize=300%2C167 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-14.png?resize=1024%2C571 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-14.png?resize=768%2C428 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-14.png?resize=600%2C334 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-14.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><br \/>\n\u56fe2\uff1a<strong>\u4e0d\u8003\u8651\u4ea4\u4e92\u4f5c\u7528\u6279\u5904\u7406\u65f6\u7684\u6279\u6b21\u6821\u6b63<\/strong><br \/>\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<br \/>\n\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<\/p>\n<p>par(mfrow = c(1,2))<br \/>\narsyn_2 &lt;- ARSyNbac(data_RNA, modelName = &#8220;RNA&#8221;, Variability = 0.95,<br \/>\nbatchEstimation = TRUE, filterNoise = FALSE, Interaction = TRUE)<br \/>\nplot(arsyn_2, typeP=&#8221;pca.cor&#8221;, bty = &#8220;L&#8221;,<br \/>\npch = custom_pch, cex = 3, col.per.group = custom_col,<br \/>\nlegend.text = c(&#8220;Color: Batch&#8221;, names(data_RNA$ListOfBatches),<br \/>\n&#8220;Fill: Cond.&#8221;, unique(colData(data_RNA$ListOfBatches$A)$tfactor)),<br \/>\nargs.legend = list(&#8220;x&#8221; = &#8220;topright&#8221;,<br \/>\n&#8220;pch&#8221; = c(NA, 15, 15, 15,<br \/>\nNA, 15, 0),<br \/>\n&#8220;col&#8221; = c(NA, &#8220;brown2&#8221;, &#8220;dodgerblue&#8221;, &#8220;forestgreen&#8221;,<br \/>\nNA, 1, 1),<br \/>\n&#8220;bty&#8221; = &#8220;n&#8221;,<br \/>\n&#8220;cex&#8221; = 1.2))<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"359\" class=\"wp-image-27740\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-15.png?resize=640%2C359\" alt=\"fig:\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-15.png?w=1400 1400w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-15.png?resize=300%2C168 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-15.png?resize=1024%2C574 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-15.png?resize=768%2C431 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-15.png?resize=600%2C336 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-15.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><br \/>\n\u56fe3\uff1a<strong>\u4ea4\u4e92\u4f5c\u7528=TRUE\u65f6\u7684\u6279\u6b21\u6821\u6b63<\/strong><br \/>\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<br \/>\n\u53f3\u56fe\uff1a\u7ecf\u8fc7\u6279\u6b21\u6761\u4ef6\u4ea4\u4e92\u6821\u6b63\u540e\u7684\u57fa\u56e0\u8868\u8fbePCA\u56fe\u8c31\u3002<br \/>\n\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<br \/>\n\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<\/p>\n<h3>ARSyNbac\u53bb\u566a<\/h3>\n<p>\u5f53batch\u672a\u88ab\u8bc6\u522b\u65f6\uff0c<strong>ARSyNbac<\/strong>\u901a\u8fc7\u8bbe\u7f6e<em>batchEstimation = FALSE<\/em>\u548c<em>filterNoise = TRUE<\/em>\u5bf9\u6b8b\u5dee\u4e2d\u7cfb\u7edf\u566a\u58f0\u7684\u5b58\u5728\u8fdb\u884c\u5206\u6790\u3002<\/p>\n<p>par(mfrow = c(1,2))<br \/>\narsyn_3 &lt;- ARSyNbac(data_RNA, modelName = &#8220;RNA&#8221;, beta = 0.5,<br \/>\nbatchEstimation = FALSE, filterNoise = TRUE)<br \/>\nplot(arsyn_3, typeP=&#8221;pca.cor&#8221;, bty = &#8220;L&#8221;,<br \/>\npch = custom_pch, cex = 3, col.per.group = custom_col,<br \/>\nlegend.text = c(&#8220;Color: Batch&#8221;, names(data_RNA$ListOfBatches),<br \/>\n&#8220;Fill: Cond.&#8221;, unique(colData(data_RNA$ListOfBatches$A)$tfactor)),<br \/>\nargs.legend = list(&#8220;x&#8221; = &#8220;topright&#8221;,<br \/>\n&#8220;pch&#8221; = c(NA, 15, 15, 15,<br \/>\nNA, 15, 0),<br \/>\n&#8220;col&#8221; = c(NA, &#8220;brown2&#8221;, &#8220;dodgerblue&#8221;, &#8220;forestgreen&#8221;,<br \/>\nNA, 1, 1),<br \/>\n&#8220;bty&#8221; = &#8220;n&#8221;,<br \/>\n&#8220;cex&#8221; = 1.2))<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"359\" class=\"wp-image-27741\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-16.png?resize=640%2C359\" alt=\"fig:\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-16.png?w=1400 1400w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-16.png?resize=300%2C168 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-16.png?resize=1024%2C575 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-16.png?resize=768%2C431 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-16.png?resize=600%2C337 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-16.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><br \/>\n\u56fe4\uff1a<strong>\u566a\u58f0\u51cf\u5c11\u6a21\u5f0f<\/strong><br \/>\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<br \/>\n\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<\/p>\n<h3>ARSyNbac\u4e24\u79cd\u6a21\u5f0f<\/h3>\n<p>\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<strong>ARSyNbac<\/strong>\u53ef\u4ee5\u901a\u8fc7\u8bbe\u7f6e<em>batchEstimation = TRUE<\/em>\u548c<em>filterNoise = TRUE<\/em>\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<\/p>\n<p>par(mfrow = c(1,2))<br \/>\narsyn_4 &lt;- ARSyNbac(data_RNA, modelName = &#8220;RNA&#8221;, beta = 0.5,<br \/>\nbatchEstimation = TRUE, filterNoise = TRUE,<br \/>\nInteraction = TRUE,<br \/>\nVariability = 0.95)<br \/>\nplot(arsyn_4, typeP=&#8221;pca.cor&#8221;, bty = &#8220;L&#8221;,<br \/>\npch = custom_pch, cex = 3, col.per.group = custom_col,<br \/>\nlegend.text = c(&#8220;Color: Batch&#8221;, names(data_RNA$ListOfBatches),<br \/>\n&#8220;Fill: Cond.&#8221;, unique(colData(data_RNA$ListOfBatches$A)$tfactor)),<br \/>\nargs.legend = list(&#8220;x&#8221; = &#8220;topright&#8221;,<br \/>\n&#8220;pch&#8221; = c(NA, 15, 15, 15,<br \/>\nNA, 15, 0),<br \/>\n&#8220;col&#8221; = c(NA, &#8220;brown2&#8221;, &#8220;dodgerblue&#8221;, &#8220;forestgreen&#8221;,<br \/>\nNA, 1, 1),<br \/>\n&#8220;bty&#8221; = &#8220;n&#8221;,<br \/>\n&#8220;cex&#8221; = 1.2))<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"359\" class=\"wp-image-27742\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-17.png?resize=640%2C359\" alt=\"fig:\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-17.png?w=1400 1400w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-17.png?resize=300%2C168 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-17.png?resize=1024%2C574 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-17.png?resize=768%2C431 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-17.png?resize=600%2C336 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-17.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><br \/>\n\u56fe5\uff1a<strong>\u4e24\u79cd\u6a21\u5f0f\u7ed3\u5408<\/strong><\/p>\n<p>\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<\/p>\n<p>\u53f3\u56fe\uff1a\u4fee\u6b63\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684PCA\u56fe\u3002<br \/>\n\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<\/p>\n<h2>\u591a\u7ec4\u5b66\u6570\u636e\u96c6\u4e0a\u7684\u6279\u6b21\u6548\u5e94\u6821\u6b63<\/h2>\n<h3>\u5173\u4e8eMultiBaC<\/h3>\n<h4>MultiBaC \u65b9\u6cd5\u6982\u8ff0<\/h4>\n<p>MultiBaC\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<br \/>\n\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<br \/>\n\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<\/p>\n<ul>\n<li>\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<\/li>\n<li>\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<\/li>\n<li>\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<\/li>\n<\/ul>\n<h2>\u793a\u4f8b\uff1a\u9175\u6bcd\u591a\u7ec4\u5b66\u6570\u636e\u96c6<\/h2>\n<p>\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[<a href=\"https:\/\/www.bioconductor.org\/packages\/release\/bioc\/vignettes\/MultiBaC\/inst\/doc\/MultiBaC.html#ref-JE1\">2<\/a>]\u3002\u5b9e\u9a8c\u5ba4B\u83b7\u5f97\u4e86\u7ffb\u8bd1\u901f\u7387\u6570\u636e\uff08RIBO\uff0c\u5b58\u53d6\u53f7GSE56622\uff09[<a href=\"https:\/\/www.bioconductor.org\/packages\/release\/bioc\/vignettes\/MultiBaC\/inst\/doc\/MultiBaC.html#ref-RIBO\">5<\/a>]\u3002\u6700\u540e\uff0c\u5b9e\u9a8c\u5ba4C\u6d4b\u91cf\u4e86\u5168\u5c40PAR-CLIP\u6570\u636e\uff08PAR-CLIP\uff0c\u5b58\u53d6\u53f7GSE43747\uff09[<a href=\"https:\/\/www.bioconductor.org\/packages\/release\/bioc\/vignettes\/MultiBaC\/inst\/doc\/MultiBaC.html#ref-PARCLIP\">6<\/a>]\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 <a href=\"https:\/\/www.bioconductor.org\/packages\/release\/bioc\/vignettes\/MultiBaC\/inst\/doc\/MultiBaC.html#fig:design\">6<\/a>\u3002<br \/>\n<img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"299\" class=\"wp-image-27743\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-18.png?resize=640%2C299\" alt=\"fig:\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-18.png?w=1400 1400w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-18.png?resize=300%2C140 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-18.png?resize=1024%2C479 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-18.png?resize=768%2C359 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-18.png?resize=600%2C281 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-18.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><br \/>\n\u56fe6\uff1a<strong>\u9175\u6bcd\u4f8b\u6570\u636e\u7ed3\u6784\u7684\u65b9\u6848<\/strong><br \/>\n\u6b64\u9175\u6bcd\u591a\u7ec4\u5b66\u6570\u636e\u5305\u542b\u5728<strong>MutiBaC<\/strong>\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 <em>data(\u201cmultiyeast\u201d)<\/em>\u6307\u4ee4\u6765\u52a0\u8f7d\u3002<\/p>\n<h3>MultiBaC\u8f93\u5165\u6570\u636e<\/h3>\n<p>\u5982\u524d\u6240\u8ff0\uff0c<strong>MultiBaC<\/strong>\u5305\u4f7f\u7528<em>MultiAssayExperiment<\/em>\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<em>data.frame<\/em>\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<em>MultiBaC<\/em>\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<em>MultiBaC<\/em>\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<em>MultiBaC<\/em>\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<br \/>\n\u8981\u751f\u6210\u4f5c\u4e3aMultiBaC\u51fd\u6570\u8f93\u5165\u7684<em>mbac<\/em>\u5bf9\u8c61\uff0c\u53ef\u4ee5\u4f7f\u7528\u5305\u4e2d\u7684<em>createMbac<\/em>\u51fd\u6570\uff0c\u8f7b\u677e\u4fbf\u6377\u5730\u5b8c\u6210\u8fd9\u9879\u4efb\u52a1\u3002<\/p>\n<p>my_mbac &lt;- createMbac (inputOmics = list(A.rna, A.gro,<br \/>\nB.rna, B.ribo,<br \/>\nC.rna, C.par),<br \/>\nbatchFactor = c(&#8220;A&#8221;, &#8220;A&#8221;,<br \/>\n&#8220;B&#8221;, &#8220;B&#8221;,<br \/>\n&#8220;C&#8221;, &#8220;C&#8221;),<br \/>\nexperimentalDesign = list(&#8220;A&#8221; = c(&#8220;Glu+&#8221;, &#8220;Glu+&#8221;,<br \/>\n&#8220;Glu+&#8221;, &#8220;Glu-&#8220;,<br \/>\n&#8220;Glu-&#8220;, &#8220;Glu-&#8220;),<br \/>\n&#8220;B&#8221; = c(&#8220;Glu+&#8221;, &#8220;Glu+&#8221;,<br \/>\n&#8220;Glu-&#8220;, &#8220;Glu-&#8220;),<br \/>\n&#8220;C&#8221; = c(&#8220;Glu+&#8221;, &#8220;Glu+&#8221;,<br \/>\n&#8220;Glu-&#8220;, &#8220;Glu-&#8220;)),<br \/>\nomicNames = c(&#8220;RNA&#8221;, &#8220;GRO&#8221;,<br \/>\n&#8220;RNA&#8221;, &#8220;RIBO&#8221;,<br \/>\n&#8220;RNA&#8221;, &#8220;PAR&#8221;))<\/p>\n<p>\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<\/p>\n<h3>MultiBaC correction<\/h3>\n<p>\u4e00\u65e6\u4f7f\u7528\u201ccreateMbac\u201d\u51fd\u6570\u521b\u5efa\u4e86<em>mbac<\/em>\u5bf9\u8c61\uff0c\u5c31\u53ef\u4ee5\u5c06\u5176\u7528\u4f5c\u201cMultiBaC\u201d\u51fd\u6570\u7684\u8f93\u5165\u6570\u636e\uff08\u4ee5<em>mbac<\/em>\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<\/p>\n<p>MultiBaC (mbac,<br \/>\ntest.comp = NULL, scale = FALSE,<br \/>\ncenter = TRUE, crossval = NULL,<br \/>\nInteraction = FALSE,<br \/>\nVariability = 0.90,<br \/>\nshowplot = TRUE,<br \/>\nshowinfo = TRUE)<\/p>\n<p><em>MultiBaC<\/em>\u51fd\u6570\u7684\u53c2\u6570\u5bf9\u5e94\u4e8eMultiBaC\u65b9\u6cd5\u7684\u5404\u4e2a\u6b65\u9aa4\uff1a<\/p>\n<ul>\n<li><strong>mbac<\/strong>: \u7531 <em>createMbac<\/em> \u751f\u6210\u7684 mbac \u5bf9\u8c61\u3002<\/li>\n<li><strong>test.comp<\/strong>: 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<\/li>\n<li><strong>scale<\/strong>: \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<\/li>\n<li><strong>center<\/strong>: \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<\/li>\n<li><strong>crossval<\/strong>: \u6574\u6570\uff1a\u4ea4\u53c9\u9a8c\u8bc1\u6bb5\u6570\u3002\u6837\u672c\u6570\uff08\u201cx\u201d\u7684\u884c\u6570\uff09\u5fc5\u987b &gt;= crossvalI\u3002\u5982\u679c\u4e3a NULL\uff08\u9ed8\u8ba4\uff09\uff0c\u5219\u6267\u884c leave-one-out \u4ea4\u53c9\u9a8c\u8bc1\u3002<\/li>\n<li><strong>Interaction<\/strong>: \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<\/li>\n<li><strong>Variability<\/strong>: \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<\/li>\n<li><strong>showplot<\/strong>: \u903b\u8f91\u503c\u3002\u5982\u679c\u4e3a TRUE\uff08\u9ed8\u8ba4\uff09\uff0c\u5219\u663e\u793a Q2 \u548c\u89e3\u91ca\u65b9\u5dee\u56fe\u3002<\/li>\n<li><strong>showinfo<\/strong>: \u903b\u8f91\u503c\u3002\u5982\u679c\u4e3a TRUE\uff08\u9ed8\u8ba4\uff09\uff0c\u5219\u663e\u793a\u51fd\u6570\u8fdb\u5ea6\u4fe1\u606f\u3002<br \/>\n\u4e0b\u9762\u663e\u793a\u4e86\u4f7f\u7528MultiBaC\u51fd\u6570\u5bf9\u9175\u6bcd\u793a\u4f8b\u6570\u636e\u8fdb\u884c\u5904\u7406\u7684\u60c5\u51b5\uff1a<\/li>\n<\/ul>\n<p>my_final_mbac &lt;- MultiBaC (my_mbac,<br \/>\ntest.comp = NULL, scale = FALSE,<br \/>\ncenter = TRUE, crossval = NULL,<br \/>\nInteraction = TRUE,<br \/>\nVariability = 0.9,<br \/>\nshowplot = TRUE,<br \/>\nshowinfo = TRUE)<br \/>\n## Step 1: Create PLS models<br \/>\n## &#8211; Model for batch A<br \/>\n## &#8211; Model for batch B<br \/>\n## &#8211; Model for batch C<br \/>\n## Step 2: Generating missing omics<br \/>\n## Step 3: Batch effect correction using ARSyNbac<br \/>\n## [1] &#8220;Table: Inner correlation between scores for each PLS model computed.&#8221;<br \/>\n##<br \/>\n##<br \/>\n## A: GRO B: RIBO C: PAR<br \/>\n## &#8212;&#8212;&#8212;&#8212;- &#8212;&#8212;&#8212;- &#8212;&#8212;&#8212;- &#8212;&#8212;&#8212;-<br \/>\n## Component: 1 0.9471967 0.9987790 0.9396986<br \/>\n## Component: 2 0.9277123 0.9991239 0.9998556<br \/>\n## Component: 3 0.9992129 1.0000000 1.0000000<br \/>\n## Component: 4 0.9999867 NA NA<br \/>\n## Component: 5 1.0000000 NA NA<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"359\" class=\"wp-image-27744\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-19.png?resize=640%2C359\" alt=\"fig:\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-19.png?w=1400 1400w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-19.png?resize=300%2C168 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-19.png?resize=1024%2C574 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-19.png?resize=768%2C431 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-19.png?resize=600%2C336 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-19.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><br \/>\n\u56fe7\uff1a<strong>Q2\u548c\u65b9\u5dee\u89e3\u91ca\u56fe<\/strong><\/p>\n<p>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<br \/>\n\u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff08<em>showinfo = TRUE<\/em>\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<em>showplot = TRUE<\/em>\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<em>MultiBaC<\/em>\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<em>Variability<\/em>\u53c2\u6570\u7684\u89e3\u91ca\u65b9\u5dee\uff08\u7070\u8272\u7684\u865a\u7ebf\uff09\u7684\u7ec4\u4ef6\u6570\u3002<\/p>\n<h3>\u9010\u6b65\u8fd0\u884cMultiBaC\u6b65\u9aa4<\/h3>\n<p><em>MultiBaC<\/em>\u7684\u6240\u6709\u4e0d\u540c\u6b65\u9aa4\u90fd\u53ef\u4ee5\u4f7f\u7528\u7279\u5b9a\u51fd\u6570\u4ece\u521d\u59cb\u7684<em>mbac<\/em>\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<br \/>\n\u4ee5\u4e0b\u662f\u60a8\u8981\u6c42\u7684\u6bb5\u843d\u7684\u7ffb\u8bd1\uff1a<\/p>\n<h4>PLS\u6a21\u578b\u62df\u5408<\/h4>\n<p>genModelList\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<\/p>\n<p>my_mbac_2 &lt;- genModelList (my_mbac, test.comp = NULL,<br \/>\nscale = FALSE, center = TRUE,<br \/>\ncrossval = NULL,<br \/>\nshowinfo = TRUE)<br \/>\n## &#8211; Model for batch A<br \/>\n## &#8211; Model for batch B<br \/>\n## &#8211; Model for batch C<\/p>\n<p><em>genModelList<\/em>\u51fd\u6570\u7684\u53c2\u6570\u4e3a\uff1a<\/p>\n<ul>\n<li><strong>mbac<\/strong>: \u5c5e\u4e8embac\u7c7b\u578b\u5bf9\u8c61\u3002<\/li>\n<li><strong>test.comp<\/strong>: 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<\/li>\n<li><strong>scale<\/strong>: \u903b\u8f91\u503c\u3002\u662f\u5426\u9700\u8981\u5bf9X\u548cY\u77e9\u9635\u8fdb\u884c\u7f29\u653e\u3002\u9ed8\u8ba4\u503c\u4e3aFALSE\u3002<\/li>\n<li><strong>center<\/strong>: \u903b\u8f91\u503c\u3002\u662f\u5426\u9700\u8981\u5bf9X\u548cY\u77e9\u9635\u8fdb\u884c\u4e2d\u5fc3\u5316\u3002\u9ed8\u8ba4\u503c\u4e3aTRUE\u3002<\/li>\n<li><strong>crossval<\/strong>: \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<\/li>\n<li><strong>showinfo<\/strong>: \u903b\u8f91\u503c\uff0c\u6307\u793a\u662f\u5426\u663e\u793a\u51fd\u6570\u8fdb\u5ea6\u4fe1\u606f\u3002\u9ed8\u8ba4\u503c\u4e3aTRUE\u3002<br \/>\n<em>genModelList<\/em>\u7684\u8f93\u51fa\u662f\u4e00\u4e2a\u5e26\u6709\u65b0\u69fd<em>PLSmodels<\/em>\u7684<em>mbac<\/em>\u5bf9\u8c61\uff0c\u8be5\u69fd\u662f\u4f7f\u7528<em>ropls<\/em>\u5305\u83b7\u5f97\u7684PLS\u6a21\u578b\u7684\u5217\u8868\u3002\u8f93\u51fa\u7684\u6bcf\u4e2a\u69fd\u5bf9\u5e94\u4e8e<em>ListOfBatches<\/em>\u4e2d\u7684\u4e00\u4e2a\u6279\u6b21\u3002\u5982\u679c\u4e00\u4e2a\u6279\u6b21\u5305\u542b\u591a\u4e2a\u975e\u516c\u5171omic\uff0c\u5219<em>genModelList<\/em>\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<\/li>\n<\/ul>\n<h4>\u7f3a\u5931Omics\u7684\u9884\u6d4b<\/h4>\n<p>\u5229\u7528genModelList\u51fd\u6570\u8f93\u51fa\u4e2d\u7684genMissingOmics\u51fd\u6570\uff0c\u5bf9\u521d\u6b65\u7f3a\u5931\u7684Omics\u8fdb\u884c\u9884\u6d4b\u3002<\/p>\n<p>multiBatchDesign &lt;- genMissingOmics(my_mbac_2)<\/p>\n<p>\u8fd0\u884c<em>genMissingOmics<\/em>\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<em>genMissingOmics<\/em>\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<\/p>\n<h4>\u6279\u6b21\u6548\u5e94\u6821\u6b63<\/h4>\n<p>my_finalwise_mbac &lt;- batchCorrection(my_mbac_2,<br \/>\nmultiBatchDesign = multiBatchDesign,<br \/>\nInteraction = TRUE,<br \/>\nVariability = 0.90)<\/p>\n<p>\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<em>CorrectedData<\/em>\u548c<em>ARSyNmodels<\/em>\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<em>ARSyNmodels<\/em>\u69fd\u5305\u542b\u6bcf\u4e2aomics\u6570\u636e\u7c7b\u578b\u7684ASCA\u5206\u89e3\u6a21\u578b\u3002<\/p>\n<h2>ARSyN\u548cMultiBaC\u7ed3\u679c\u7684\u53ef\u89c6\u5316<\/h2>\n<p>\u5982\u524d\u6240\u8ff0\uff0c<em>ARSyNbac<\/em>\u548c<em>MultiBaC<\/em>\u7684\u8f93\u51fa\u662f<em>mbac<\/em>\u7c7b\u578b\u7684\u5bf9\u8c61\u3002\u7531\u4e8e<em>mbac<\/em>\u7c7b\u5305\u542b\u7ed8\u56fe\u65b9\u6cd5\uff0c\u56e0\u6b64\u53ef\u4ee5\u5c06<em>plot\u51fd\u6570\u5e94\u7528\u4e8e<\/em>mbac<em>\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<\/em>mbac<em>\u5bf9\u8c61\u7684<\/em>plot*\u51fd\u6570\u63a5\u53d7\u51e0\u4e2a\u989d\u5916\u7684\u53c2\u6570\uff1a<\/p>\n<p>plot (x, typeP = &#8220;def&#8221;,<br \/>\ncol.by.batch = TRUE,<br \/>\ncol.per.group = NULL,<br \/>\ncomp2plot = c(1,2),<br \/>\nlegend.text = NULL,<br \/>\nargs.legend = NULL, &#8230;)<\/p>\n<p>\u63cf\u8ff0\u53c2\u6570\uff1a<\/p>\n<ul>\n<li><strong>x<\/strong>: \u7531<em>MultiBaC<\/em>\u65b9\u6cd5\u8fd4\u56de\u7684\u201cmbac\u201d\u7c7b\u5bf9\u8c61\u3002<\/li>\n<li><strong>typeP<\/strong>: \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<\/li>\n<li><strong>col.by.batch<\/strong>: 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<\/li>\n<li><strong>col.per.group<\/strong>: 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<\/li>\n<li><strong>comp2plot<\/strong>: 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<\/li>\n<li><strong>legend.text<\/strong>: \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<\/li>\n<li><strong>args.legend<\/strong>: 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<\/li>\n<li><strong>\u2026<\/strong>: \u5176\u4ed6\u56fe\u5f62\u53c2\u6570\u3002<br \/>\n\u867d\u7136 <em>plot<\/em> \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<em>Q2_plot (mbac)<\/em>\u3001<em>explained_varPlot (mbac)<\/em>\u3001<em>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)<\/em>\u3001<em>batchEstPlot (mbac)<\/em>\u4ee5\u53ca <em>inner_relPlot (mbac, comp2plot = c(1,2))<\/em>.<br \/>\n\u6240\u6709\u8fd9\u4e9b\u56fe\u90fd\u6709\u52a9\u4e8e\u9a8c\u8bc1\u548c\u7406\u89e3<em>MultiBaC<\/em>\u6216<em>ARSyNbac<\/em>\u7684\u6027\u80fd\u3002\u6240\u6709\u8fd9\u4e9b\u56fe\u90fd\u53ef\u4ee5\u4f7f\u7528<em>MultiBaC<\/em>\u7684\u8f93\u51fa\uff0c\u800c\u663e\u793a\u4e0ePLS\u6a21\u578b\u76f8\u5173\u7684\u4fe1\u606f\u56fe\u5219\u4e0d\u9002\u7528\u4e8e<em>ARSyNbac<\/em>\u7684\u8f93\u51fa\uff08\u8bf7\u53c2\u89c1<em>typeP<\/em>\u53c2\u6570\uff09\u3002<br \/>\n\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<\/li>\n<\/ul>\n<h2>PLS\u6a21\u578b\u4e2d\u7684\u5185\u90e8\u76f8\u5173\u6027<\/h2>\n<p>\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<\/p>\n<p>plot (my_final_mbac, typeP = &#8220;inner&#8221;, comp2plot = c(1,2))<br \/>\n## Hit &lt;Return&gt; to see next plot:<br \/>\n## Inner correlation of scores. Batch: A; Model for omic: GRO<br \/>\n## Warning in par(initpar): graphical parameter &#8220;cin&#8221; cannot be set<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"358\" class=\"wp-image-27745\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-20.png?resize=640%2C358\" alt=\"fig:\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-20.png?w=1400 1400w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-20.png?resize=300%2C168 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-20.png?resize=1024%2C573 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-20.png?resize=768%2C430 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-20.png?resize=600%2C336 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-20.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><br \/>\n\u56fe8\uff1a<strong>PLS\u7ec4\u4ef6\u5185\u90e8\u5173\u7cfb\u7684\u7ed8\u56fe<\/strong><br \/>\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<br \/>\n\u5982\u56fe<a href=\"https:\/\/www.bioconductor.org\/packages\/release\/bioc\/vignettes\/MultiBaC\/inst\/doc\/MultiBaC.html#fig:inner\">8<\/a>\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\u56fe<a href=\"https:\/\/www.bioconductor.org\/packages\/release\/bioc\/vignettes\/MultiBaC\/inst\/doc\/MultiBaC.html#fig:inner\">8<\/a>\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<\/p>\n<h2>\u6279\u6b21\u6548\u5e94\u4f30\u8ba1\u56fe<\/h2>\n<p>\u6b64\u56fe\u663e\u793a\u4e86\u4f30\u8ba1\u6279\u6b21\u6548\u5e94\u7684\u5e45\u5ea6\u3002\u901a\u5e38\uff0c\u5728\u6267\u884c<em>MultiBaC<\/em>\u6216<em>ARSyNbac<\/em>\u4e4b\u524d\u4f7f\u7528\u6b64\u56fe\uff0c\u56e0\u4e3a\u5b83\u53ea\u9700\u8981<em>createMbac<\/em>\u51fd\u6570\u8fd4\u56de\u7684<em>mbac<\/em>\u57fa\u672c\u6570\u636e\u3002<\/p>\n<p>plot (my_final_mbac, typeP = &#8220;batch&#8221;)<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"373\" class=\"wp-image-27746\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-21.png?resize=640%2C373\" alt=\"fig:\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-21.png?w=1400 1400w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-21.png?resize=300%2C175 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-21.png?resize=1024%2C597 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-21.png?resize=768%2C448 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-21.png?resize=600%2C350 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-21.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><br \/>\n\u56fe9\uff1a<strong>\u6279\u6b21\u6548\u5e94\u4f30\u8ba1\u56fe<\/strong><\/p>\n<p>\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<br \/>\n\u9175\u6bcd\u4f8b\u5b50\u7684\u7406\u8bba\u6279\u6b21\u6548\u5e94\u5e45\u5ea6\u5728\u56fe <a href=\"https:\/\/www.bioconductor.org\/packages\/release\/bioc\/vignettes\/MultiBaC\/inst\/doc\/MultiBaC.html#fig:batchest\">9<\/a> \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<br \/>\n\u4ee5\u4e0b\u662fPCA\u56fe\u8868\u7684\u4e2d\u6587\u7ffb\u8bd1\u3002<\/p>\n<h2>PCA\u56fe<\/h2>\n<p>\u53ef\u4ee5\u901a\u8fc7\u6bd4\u8f83\u4fee\u6b63\u524d\u540e\u7684PCA\u56fe\u6765\u8bc4\u4f30<em>ARSyNbac<\/em>\u6216<em>MultiBaC<\/em>\u4fee\u6b63\u7684\u6548\u679c\u3002\u5bf9\u4e8e<em>MultiBaC<\/em>\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<br \/>\n\u8fd9\u4e9bPCA\u56fe\u5bf9\u4e8e<em>ARSyNbac<\/em>\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<em>\u201ctypeP = pca.org\u201d<\/em>\u6216<em>\u201ctypeP = pca.cor\u201d<\/em>\u3002<\/p>\n<p>plot (my_final_mbac, typeP = &#8220;pca.org&#8221;,<br \/>\ncex.axis = 1, cex.lab = 1, cex = 3, bty = &#8220;L&#8221;,<br \/>\ncex.main = 1.2, pch = 19)<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"356\" class=\"wp-image-27747\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-22.png?resize=640%2C356\" alt=\"fig:\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-22.png?w=1400 1400w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-22.png?resize=300%2C167 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-22.png?resize=1024%2C569 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-22.png?resize=768%2C427 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-22.png?resize=600%2C333 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-22.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><br \/>\n\u56fe10\uff1a<strong>\u5728\u539f\u59cb\u6570\u636e\u4e0a\u6267\u884cPCA\u5f97\u5230\u7684\u4e3b\u6210\u5206\u56fe<\/strong><\/p>\n<p>plot (my_final_mbac, typeP = &#8220;pca.cor&#8221;,<br \/>\ncex.axis = 1, cex.lab = 1, cex = 3, bty = &#8220;L&#8221;,<br \/>\ncex.main = 1.2, pch = 19)<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"356\" class=\"wp-image-27748\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-23.png?resize=640%2C356\" alt=\"fig:\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-23.png?w=1400 1400w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-23.png?resize=300%2C167 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-23.png?resize=1024%2C570 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-23.png?resize=768%2C427 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-23.png?resize=600%2C334 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-23.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><br \/>\n\u56fe11\uff1a\u4fee\u6b63\u6570\u636e\u4e0a\u7684\u4e3b\u6210\u5206\u5206\u6790\uff08PCA\uff09\u56fe\uff08\u9ed8\u8ba4\u8bbe\u7f6e\uff09<br \/>\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<em>col.per.group<\/em>\u548c<em>pch<\/em>\u53c2\u6570\u3002\u56fe<a href=\"https:\/\/www.bioconductor.org\/packages\/release\/bioc\/vignettes\/MultiBaC\/inst\/doc\/MultiBaC.html#fig:pcaplot2\">12<\/a>\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<em>comp2plot<\/em>\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<em>legend.text<\/em>\u548c<em>args.legend<\/em>\u3002\u901a\u8fc7<em>legend.text<\/em>\uff0c\u6211\u4eec\u6307\u793a\u56fe\u4f8b\u7684\u6587\u672c\u6807\u7b7e\uff0c\u5176\u4f59\u56fe\u4f8b\u53c2\u6570\u4fdd\u5b58\u5728<em>args.legend<\/em>\uff08x\uff0cy\uff0cpch\uff0cfill\uff0ccol\uff0cbty\u7b49)\u4e2d\u3002\u5982\u679c\u5411\u51fd\u6570\u63d0\u4f9b<em>legend.text<\/em>\uff0c\u5219\u4e0d\u8003\u8651<em>args.legend<\/em>\u3002<\/p>\n<p>custom_col &lt;- c(&#8220;brown2&#8221;, &#8220;dodgerblue&#8221;, &#8220;forestgreen&#8221;)<br \/>\ncustom_pch &lt;- c(19,19,19,1,1,1,15,15,15,0,0,0, # batch A<br \/>\n19,19,1,1,17,17,2,2, # batch B<br \/>\n19,19,1,1,18,18,5,5) # batch C<\/p>\n<p>plot(my_final_mbac, typeP = &#8220;pca.both&#8221;, col.by.batch = TRUE,<br \/>\ncol.per.group = custom_col, comp2plot = 1:3,<br \/>\ncex.axis = 1.3, cex.lab = 1.2, cex = 3, bty = &#8220;L&#8221;,<br \/>\ncex.main = 1.7, pch = custom_pch,<br \/>\nlegend.text = c(&#8220;Color&#8221;, names(my_final_mbac$ListOfBatches),<br \/>\n&#8220;Shape&#8221;, c(&#8220;RNA&#8221;, &#8220;GRO&#8221;, &#8220;RIBO&#8221;, &#8220;PAR&#8221;),<br \/>\n&#8220;Fill&#8221;, levels(colData(my_final_mbac$ListOfBatches$A)$tfactor)),<br \/>\nargs.legend = list(&#8220;x&#8221; = &#8220;topright&#8221;,<br \/>\n&#8220;pch&#8221; = c(NA, 15, 15, 15,<br \/>\nNA, 19, 15, 17, 18,<br \/>\nNA, 19, 1),<br \/>\n&#8220;col&#8221; = c(NA, &#8220;brown2&#8221;, &#8220;dodgerblue&#8221;, &#8220;forestgreen&#8221;,<br \/>\nNA, rep(1, 4),<br \/>\nNA, 1, 1),<br \/>\n&#8220;bty&#8221; = &#8220;n&#8221;,<br \/>\n&#8220;cex&#8221; = 2))<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"505\" class=\"wp-image-27749\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-24.png?resize=640%2C505\" alt=\"fig:\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-24.png?w=1400 1400w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-24.png?resize=300%2C237 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-24.png?resize=1024%2C808 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-24.png?resize=768%2C606 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-24.png?resize=600%2C474 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/fig-24.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><br \/>\n\u56fe12\uff1a<strong>\u5b9a\u5236\u7684\u4e3b\u6210\u5206\u5206\u6790\u56fe<\/strong><br \/>\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<br \/>\n\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<\/p>\n<h2>\u603b\u7ed3<\/h2>\n<p>MultiBaC\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<\/p>\n<h2>\u53c2\u8003\u6587\u732e<\/h2>\n<ol>\n<li>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.<\/li>\n<li>Pelechano V, P\u00e9rez-Ort\u00edn JE. There is a steady-state transcriptome in exponentially growing yeast cells. Yeast. 2010;27:413\u201322. doi:<a href=\"https:\/\/doi.org\/10.1002\/yea.1768\">10.1002\/yea.1768<\/a>.<\/li>\n<li>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:<a href=\"https:\/\/doi.org\/10.1016\/j.molcel.2004.06.004\">10.1016\/j.molcel.2004.06.004<\/a>.<\/li>\n<li>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:<a href=\"https:\/\/doi.org\/10.1371\/journal.pone.0015442\">10.1371\/journal.pone.0015442<\/a>.<\/li>\n<li>Zid BM, O\u2019Shea EK. Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast. Nature. 514:117\u201321. doi:<a href=\"https:\/\/doi.org\/10.1038\/nature13578\">10.1038\/nature13578<\/a>.<\/li>\n<li>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:<a href=\"https:\/\/doi.org\/10.1186\/gb-2013-14-2-r13\">10.1186\/gb-2013-14-2-r13<\/a>.<\/li>\n<\/ol>\n<p>\u5982\u679c\u5c0f\u4f19\u4f34\u6709\u5176\u4ed6\u6570\u636e\u5206\u6790\u9700\u6c42\uff0c\u53ef\u4ee5\u5c1d\u8bd5\u4f7f\u7528\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u751f\u4fe1\u5206\u6790\u5c0f\u5de5\u5177\u4e91\u5e73\u53f0\uff0c\u96f6\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u975e\u5e38\u65b9\u4fbf\u5965\uff0c\u4e91\u5e73\u53f0\u7f51\u5740\u4e3a\uff1a(<a href=\"http:\/\/www.biocloudservice.com\/home.html\">http:\/\/www.biocloudservice.com\/home.html<\/a>)\uff0c\u5176\u4e2d\u4e5f\u5305\u62ec\u4e86\u901a\u8def\u8868\u8fbe\u5206\u6790(<a href=\"http:\/\/www.biocloudservice.com\/313\/313.php\">http:\/\/www.biocloudservice.com\/313\/313.php<\/a>)\uff0c\u5355\u7ec6\u80de\u7684\u57fa\u56e0\u5171\u8868\u8fbe\u5206\u6790(<a href=\"http:\/\/www.biocloudservice.com\/906\/906.php\">http:\/\/www.biocloudservice.com\/906\/906.php<\/a>)\u7b49\u5404\u79cd\u5c0f\u5de5\u5177\u54e6~\uff0c\u6709\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u767b\u5f55\u7f51\u7ad9\u8fdb\u884c\u4e86\u89e3\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u5728\u751f\u7269\u4fe1\u606f\u5b66\u9886\u57df\uff0c\u968f\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 [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/27736"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=27736"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/27736\/revisions"}],"predecessor-version":[{"id":27750,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/27736\/revisions\/27750"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=27736"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=27736"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=27736"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}