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0.5px;\"><strong><span style=\"font-size: 15px;\">\u751f\u4fe1\u4ebaR\u8bed\u8a00\u5b66\u4e60\u5fc5\u5907<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u7acb\u523b\u62e5\u6709\u4e00\u4e2aRstudio\u8d26\u53f7<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u5f00\u542f\u5347\u7ea7\u6a21\u5f0f\u5427<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"color: rgb(255, 129, 36);font-size: 12px;letter-spacing: 0.5px;\">\uff0856\u7ebf\u7a0b\uff0c256G\u5185\u5b58\uff0c\u4e2a\u4eba\u5b58\u50a81T\uff09<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: 29.9652%;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 29.9652% 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data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<section style=\"display: contents;\" powered-by=\"xiumi.us\">\n<section style=\"display: contents;\">\n<section style=\"display: contents;\">\n<section style=\"height: 0px;overflow: hidden;\"><span style=\"font-size: 14px;letter-spacing: 0.578px;caret-color: red;\"> <\/span><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><span style=\"text-align: left;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\">\u57fa\u56e0\u6570\u636e\u7684\u5dee\u5f02\u6027\u5206\u6790\u662f\u4e00\u79cd\u9488\u5bf9\u4e0d\u540c\u751f\u7269\u6837\u672c\u6216\u4e0d\u540c\u5904\u7406\u6761\u4ef6\u4e0b\u57fa\u56e0\u8868\u8fbe\u91cf\u53d8\u5316\u7684\u5206\u6790\u65b9\u6cd5\u3002\u5b83\u53ef\u4ee5\u7528\u6765\u8bc6\u522b\u57fa\u56e0\u5728\u4e24\u4e2a\u6216\u591a\u4e2a\u6837\u672c\u4e4b\u95f4\u7684\u8868\u8fbe\u5dee\u5f02\uff0c\u4ece\u800c\u5e2e\u52a9\u6211\u4eec\u4e86\u89e3\u57fa\u56e0\u5728\u4e0d\u540c\u751f\u7269\u72b6\u6001\u4e0b\u7684\u529f\u80fd\u548c\u8c03\u63a7\u673a\u5236\u3002\u5bf9\u4e8e\u57fa\u56e0\u82af\u7247\u7684\u5dee\u5f02\u8868\u8fbe\u5206\u6790\uff0c\u7531\u4e8e\u5176\u6570\u636e\u666e\u904d\u88ab\u8ba4\u4e3a\u670d\u4ece\u6b63\u6001\u5206\u5e03\uff0c\u56e0\u6b64\u5e38\u7528\u7684\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u65b9\u6cd5\u662f\u5728\u6bcf\u4e2a\u57fa\u56e0\u4e0a\u5e94\u7528<\/span><span style=\"text-align: left;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\">t<\/span><span style=\"text-align: left;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\">\u68c0\u9a8c\u6216\u65b9\u5dee\u5206\u6790\u3002\u800c\u9ad8\u901a\u91cf\u5206\u6790\u6d89\u53ca\u5230\u591a\u4e2a\u57fa\u56e0\u7684\u540c\u65f6\u68c0\u9a8c\uff0c\u56e0\u6b64\u9700\u8981\u8fdb\u884c\u591a\u91cd\u6bd4\u8f83\u6821\u6b63\uff0c\u4ee5\u63a7\u5236\u5047\u9633\u6027\u7684\u53d1\u751f\u3002<\/span><br \/><\/p>\n<\/section>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u57fa\u56e0\u6570\u636e\u7684\u5dee\u5f02\u6027\u5206\u6790\u901a\u5e38\u5305\u62ec\u4ee5\u4e0b\u6b65\u9aa4\uff1a<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u6570\u636e\u9884\u5904\u7406\uff1a\u5305\u62ec\u5bf9\u539f\u59cb\u6570\u636e\u8fdb\u884c\u8d28\u91cf\u63a7\u5236\u3001\u53bb\u9664\u6389\u4f4e\u8d28\u91cf\u7684\u57fa\u56e0\u548c\u6837\u672c\u3001\u8fdb\u884c\u5f52\u4e00\u5316\u7b49\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><span style=\"font-size: 14px;\">\u5dee\u5f02\u6027\u5206\u6790\uff1a\u901a\u8fc7\u7edf\u8ba1\u5b66\u65b9\u6cd5\uff08\u5982<\/span>t<span style=\"font-size: 14px;\">\u68c0\u9a8c\u3001\u65b9\u5dee\u5206\u6790\u3001<\/span><span style=\"font-size: 14px;\">Wilcoxon<\/span><span style=\"font-size: 14px;\">\u68c0\u9a8c\u7b49\uff09\u6216\u673a\u5668\u5b66\u4e60\u65b9\u6cd5\uff08\u5982\u652f\u6301\u5411\u91cf\u673a\u3001\u968f\u673a\u68ee\u6797\u7b49\uff09\u6765\u6bd4\u8f83\u4e0d\u540c\u6837\u672c\u4e4b\u95f4\u7684\u57fa\u56e0\u8868\u8fbe\u91cf\uff0c\u627e\u51fa\u8868\u8fbe\u91cf\u663e\u8457\u5dee\u5f02\u7684\u57fa\u56e0\u3002\u5dee\u5f02\u6027\u5206\u6790\u7684\u7ed3\u679c\u53ef\u4ee5\u7528<\/span><span style=\"font-size: 14px;\">Volcano<\/span><span style=\"font-size: 14px;\">\u56fe\u6216<\/span><span style=\"font-size: 14px;\">Heatmap<\/span><span style=\"font-size: 14px;\">\u7b49\u65b9\u5f0f\u8fdb\u884c\u53ef\u89c6\u5316\u5c55\u793a\uff0c\u4ee5\u4fbf\u66f4\u597d\u5730\u7406\u89e3\u5dee\u5f02\u57fa\u56e0\u7684\u7279\u70b9\u548c\u8868\u8fbe\u6a21\u5f0f\u3002<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u529f\u80fd\u5bcc\u96c6\u5206\u6790\uff1a\u5bf9\u5dee\u5f02\u57fa\u56e0\u8fdb\u884c\u529f\u80fd\u5bcc\u96c6\u5206\u6790\uff0c\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u4e86\u89e3\u8fd9\u4e9b\u57fa\u56e0\u5728\u751f\u7269\u5b66\u8fc7\u7a0b\u3001\u901a\u8def\u3001\u529f\u80fd\u548c\u75be\u75c5\u4e2d\u7684\u4f5c\u7528\u548c\u8c03\u63a7\u673a\u5236\u3002\u529f\u80fd\u5bcc\u96c6\u5206\u6790\u65b9\u6cd5\u5305\u62ec\u57fa\u56e0\u672c\u4f53\u8bba\u5206\u6790\u3001\u5bcc\u96c6\u5206\u6790\u3001\u901a\u8def\u5206\u6790\u7b49\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u7ed3\u679c\u89e3\u91ca\u548c\u9a8c\u8bc1\uff1a\u57fa\u4e8e\u5dee\u5f02\u6027\u5206\u6790\u548c\u529f\u80fd\u5bcc\u96c6\u5206\u6790\u7684\u7ed3\u679c\uff0c\u53ef\u4ee5\u8fdb\u4e00\u6b65\u8fdb\u884c\u5b9e\u9a8c\u9a8c\u8bc1\uff0c\u4ee5\u786e\u5b9a\u5dee\u5f02\u57fa\u56e0\u7684\u751f\u7269\u5b66\u610f\u4e49\u548c\u529f\u80fd\uff0c\u4ece\u800c\u66f4\u597d\u5730\u7406\u89e3\u57fa\u56e0\u5728\u4e0d\u540c\u751f\u7269\u72b6\u6001\u4e0b\u7684\u4f5c\u7528\u548c\u8c03\u63a7\u673a\u5236\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">DESeq2<span style=\"font-size: 14px;\">\uff0c<\/span><span style=\"font-size: 14px;\">EdgeR<\/span><span style=\"font-size: 14px;\">\u548c<\/span><span style=\"font-size: 14px;\">limma<\/span><span style=\"font-size: 14px;\">\u662f\u4e09\u79cd<\/span><span style=\"font-size: 14px;\">R<\/span><span style=\"font-size: 14px;\">\u8bed\u8a00\u4e2d\u5e38\u7528\u7684\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u5de5\u5177\u5305\uff0c\u53ef\u4ee5\u7528\u4e8e\u5206\u6790<\/span><span style=\"font-size: 14px;\">RNA-seq<\/span><span style=\"font-size: 14px;\">\u6216<\/span><span style=\"font-size: 14px;\">microarray<\/span><span style=\"font-size: 14px;\">\u7b49\u9ad8\u901a\u91cf\u6570\u636e\u7684\u5dee\u5f02\u8868\u8fbe\u3002<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/span><\/p>\n<p><span style=\"text-decoration: underline;\"><strong><span style=\"text-decoration: underline;font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;color: rgb(61, 170, 214);\">DESeq2\uff1a<\/span><\/strong><\/span><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u4e00\u822c\u5dee\u5f02\u5206\u6790\u8f6f\u4ef6\u5982DESeq2\u548cedgeR\u7684\u539f\u7406\u662f\u6bd4\u8f83\u7ec4\u95f4\u5dee\u5f02\u548c\u7ec4\u5185\u5dee\u5f02\u3002\u6240\u4ee5\u8bf4\u901a\u5e38\u60c5\u51b5\u4e0b\uff0c\u5982\u679c\u6ca1\u6709\u91cd\u590d\uff0c\u5219\u7ec4\u5185\u5dee\u5f02\u65e0\u6cd5\u8ba1\u7b97\u3002DESeq2\u91c7\u7528\u6570\u636e\u5f52\u4e00\u5316\u548c\u53bb\u9664\u6279\u6b21\u6548\u5e94\u7684\u65b9\u6cd5\uff0c\u4ee5\u6d88\u9664\u6837\u672c\u4e4b\u95f4\u7684\u6280\u672f\u53d8\u5f02\u3002\u5b83\u901a\u8fc7\u5bf9\u6837\u672c\u4e2d\u7684\u57fa\u56e0\u8ba1\u6570\u6570\u636e\u8fdb\u884c\u8d1f\u4e8c\u9879\u5f0f\u6a21\u578b\u62df\u5408\uff0c\u6765\u9274\u5b9a\u57fa\u56e0\u5728\u4e0d\u540c\u6837\u672c\u4e4b\u95f4\u7684\u8868\u8fbe\u5dee\u5f02\u5e76\u8fdb\u884c\u5dee\u5f02\u57fa\u56e0\u7684\u7edf\u8ba1\u663e\u8457\u6027\u68c0\u9a8c\u3002\u540c\u65f6\u4e5f\u53ef\u7528\u4e8e\u8003\u8651\u751f\u7269\u5b66\u91cd\u590d\u7684\u5f71\u54cd\uff0c\u4ece\u800c\u66f4\u51c6\u786e\u5730\u4f30\u8ba1\u57fa\u56e0\u8868\u8fbe\u91cf\u7684\u65b9\u5dee\u548c\u6807\u51c6\u8bef\u5dee\u3002DESeq2\u4f7f\u7528Wald\u68c0\u9a8c\u6765\u9274\u5b9a\u5dee\u5f02\u57fa\u56e0\uff0c\u5e76\u4f7f\u7528Benjamini-Hochberg\u65b9\u6cd5\u6765\u8fdb\u884c\u591a\u91cd\u68c0\u9a8c\u6821\u6b63\u3002\u53e6\u5916\uff0cDESeq2\u8fd8\u63d0\u4f9b\u4e86\u591a\u79cd\u53ef\u89c6\u5316\u65b9\u6cd5\uff0c\u5982MA\u56fe\u3001Heatmap\u548cPCA\u5206\u6790\u7b49\u3002<\/span><\/p>\n<p><br \/><\/p>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<h1 style=\"text-align: center;\"><em style=\"letter-spacing: 0.034em;\"><\/em><\/h1>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"properties\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">##DESeq\u5dee\u5f02\u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attr\">dds<\/span> <span class=\"code-snippet__string\"><- estimateSizeFactors(dds) \u8ba1\u7b97\u5f52\u4e00\u5316\u7cfb\u6570sizeFactor<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attr\">dds<\/span> <span class=\"code-snippet__string\"><- estimateDispersions(dds) \u4f30\u8ba1\u57fa\u56e0\u7684\u79bb\u6563\u7a0b\u5ea6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attr\">dds <- nbinomWaldTest(dds) \u7edf\u8ba1\u68c0\u9a8c\uff0c\u5dee\u5f02\u5206\u6790<\/span><\/span><\/code><\/pre>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.7729941291585127\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_fbe9QCNicZ8pvexHphqjEM1kiaq9eg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxkQdNGeWtDGfzAUzolwgtQ6CVCxLmR3W3mIUWH61esJLY6mdfbe9QCNicZ8pvexHphqjEM1kiaq9eg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"511\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">EdgeR\uff1a\u9002\u7528\u4e8eRNA-seq\u548cmicroarray\u6570\u636e\u3002\u4f7f\u7528\u8d1f\u4e8c\u9879\u5f0f\u6a21\u578b\u6765\u5bf9\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u8fdb\u884c\u5efa\u6a21\uff0c\u4f7f\u7528TMM\uff08trimmed mean of M values\uff09\u65b9\u6cd5\u8fdb\u884c\u6570\u636e\u5f52\u4e00\u5316\u3002EdgeR\u4f7f\u7528exact test\u6216quasi-likelihood F-test\u6765\u8fdb\u884c\u5dee\u5f02\u5206\u6790\u3002\u540c\u65f6\uff0c\u5b83\u4e5f\u4f7f\u7528Benjamini-Hochberg\u65b9\u6cd5\u6765\u8fdb\u884c\u591a\u91cd\u68c0\u9a8c\u6821\u6b63\u3002edgeR\u6709\u4e00\u90e8\u5206\u529f\u80fd\u662f\u4f9d\u8d56\u4e8elimma\u5305\u3002<\/span><span style=\"mso-spacerun:'yes';font-family:Calibri;mso-fareast-font-family:\u5b8b\u4f53;mso-bidi-font-family:'Times New Roman';\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"white-space:pre-wrap;font-family: Consolas, "Liberation Mono", Menlo, Courier, monospace;font-size: 14px;background-color: rgb(250, 250, 250);color: rgb(51, 51, 51);letter-spacing: 0.034em;\">\u200d<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.7148936170212766\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_LWB3EVicnMW1xq61QlNgmULiawmJBg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxkQdNGeWtDGfzAUzolwgtQEhxibWUObuywxdueic35MOxicqyzpLWB3EVicnMW1xq61QlNgmULiawmJBg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"470\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">limma\uff1a\u76ee\u524d\u5728\u57fa\u56e0\u82af\u7247\u7684\u5206\u6790\u7528\u7684\u6700\u591a\u7684\u5c31\u662flimma\u3002\u867d\u7136\u5b83\u662f\u9488\u5bf9\u82af\u7247\u6570\u636e\u5f00\u53d1\u7684\uff0c\u4f46\u4e5f\u6709limma-voom\u53ef\u4ee5\u5206\u6790\u8f6c\u5f55\u7ec4\u6570\u636e\u3002\u5728\u5904\u7406RNA-Seq\u6570\u636e\u65f6\uff0craw read count\u5148\u88ab\u8f6c\u6210log2-counts-per-million (logCPM)\uff0c\u7136\u540e\u5bf9mean-variance\u5173\u7cfb\u5efa\u6a21\u3002limma\u4f7f\u7528\u7ebf\u6027\u6a21\u578b\u6765\u5206\u6790microarray\u548cRNA-seq\u6570\u636e\u3002\u901a\u8fc7\u7ecf\u9a8cBayes\u65b9\u6cd5\u6765\u8c03\u6574\u57fa\u56e0\u8868\u8fbe\u503c\uff0c\u4ee5\u63d0\u9ad8\u5dee\u5f02\u57fa\u56e0\u7684\u68c0\u6d4b\u80fd\u529b\uff0c\u5e76\u4f7f\u7528FDR\u63a7\u5236\u65b9\u6cd5\u8fdb\u884c\u591a\u91cd\u68c0\u9a8c\u6821\u6b63\u3002limma\u4e5f\u63d0\u4f9b\u4e86\u8bb8\u591a\u53ef\u89c6\u5316\u65b9\u6cd5\uff0c\u5982MA\u56fe\u3001Heatmap\u548cVolcano\u56fe\u7b49\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5c0f\u679c\u4ee5limma\u4e3a\u4f8b\uff0c\u5e26\u5927\u5bb6\u5b9e\u8df5\u4e00\u4e0b\u5427\uff5e<\/span><span style=\"mso-spacerun:'yes';font-family:Calibri;mso-fareast-font-family:\u5b8b\u4f53;mso-bidi-font-family:'Times New Roman';\"><o:p><\/o:p><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"properties\"><code><span class=\"code-snippet_outer\">design <- model.matrix(~0+group+lane)<\/span><\/code><code><span class=\"code-snippet_outer\">colnames(design) <- gsub(\"group\", \"\", colnames(design))<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">contr.matrix <- makeContrasts(<\/span><\/code><code><span class=\"code-snippet_outer\"> BasalvsLP = Basal-LP, <\/span><\/code><code><span class=\"code-snippet_outer\"> BasalvsML = Basal - ML, <\/span><\/code><code><span class=\"code-snippet_outer\"> LPvsML = LP - ML, <\/span><\/code><code><span class=\"code-snippet_outer\"> levels = colnames(design))<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">par(mfrow=c(1,2))<\/span><\/code><code><span class=\"code-snippet_outer\">v <- voom(x, design, plot=TRUE)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">vfit <- lmFit(v, design)<\/span><\/code><code><span class=\"code-snippet_outer\">vfit <- contrasts.fit(vfit, contrasts=contr.matrix)<\/span><\/code><code><span class=\"code-snippet_outer\">efit <- eBayes(vfit)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">summary(decideTests(efit))<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">tfit <- treat(vfit, lfc=1)<\/span><\/code><code><span class=\"code-snippet_outer\">dt <- decideTests(tfit)<\/span><\/code><code><span class=\"code-snippet_outer\">summary(dt)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">de.common <- which(dt[,1]!=0 & dt[,2]!=0)<\/span><\/code><code><span class=\"code-snippet_outer\">length(de.common)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">vennDiagram(dt[,1:2], circle.col=c(\"turquoise\", \"salmon\")<\/span><\/code><code><span class=\"code-snippet_outer\">#\u97e6\u6069\u56fe\u5c55\u793a\u4e86\u4ec5basal\u548cLP\uff08\u5de6\uff09\u3001\u4ec5basal\u548cML\uff08\u53f3\uff09\u7684\u5bf9\u6bd4\u7684DE\u57fa\u56e0\u6570\u91cf\uff0c\u8fd8\u6709\u4e24#\u79cd\u5bf9\u6bd4\u4e2d\u5171\u540c\u7684DE\u57fa\u56e0\u6570\u91cf\uff08\u4e2d\uff09\u3002\u5728\u4efb\u4f55\u5bf9\u6bd4\u4e2d\u5747\u4e0d\u5dee\u5f02\u8868\u8fbe\u7684\u57fa\u56e0\u6570\u91cf\u6807\u4e8e\u53f3\u4e0b\u3002<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.7923076923076923\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_N6L66N3rC0KYPfjJUPNLnZXfjWt2nw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxkQdNGeWtDGfzAUzolwgtQvddzpJ4xRRvaBHn3mMH0dCLVN6L66N3rC0KYPfjJUPNLnZXfjWt2nw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"390\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"bash\"><code><span class=\"code-snippet_outer\">library(gplots)<\/span><\/code><code><span class=\"code-snippet_outer\">basal.vs.lp.topgenes <- basal.vs.lp$ENTREZID[1:100]<\/span><\/code><code><span class=\"code-snippet_outer\">i <- which(v$genes$ENTREZID %in% basal.vs.lp.topgenes)<\/span><\/code><code><span class=\"code-snippet_outer\">mycol <- colorpanel(1000,\"blue\",\"white\",\"red\")<\/span><\/code><code><span class=\"code-snippet_outer\">heatmap.2(lcpm[i,], scale=\"row\",<\/span><\/code><code><span class=\"code-snippet_outer\"> labRow=v$genes$SYMBOL[i], labCol=group, <\/span><\/code><code><span class=\"code-snippet_outer\"> col=mycol, trace=\"none\", density.info=\"none\", <\/span><\/code><code><span class=\"code-snippet_outer\"> margin=c(8,6), lhei=c(2,10), dendrogram=\"column\"<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u5728basal\u548cLP\u7684\u5bf9\u6bd4\u4e2d\u524d100\u4e2aDE\u57fa\u56e0log-CPM\u503c\u7684\u70ed\u56fe\u3002\u8c03\u6574\u540e\uff0c\u6bcf\u4e2a\u57fa\u56e0\uff08\u6bcf\u884c\uff09#\u7684\u8868\u8fbe\u5747\u503c\u4e3a0\uff0c\u5e76\u4e14\u6807\u51c6\u5dee\u4e3a1\u3002\u7ed9\u5b9a\u57fa\u56e0\u76f8\u5bf9\u9ad8\u8868\u8fbe\u7684\u6837\u672c\u88ab\u6807\u8bb0\u4e3a\u7ea2\u8272\uff0c\u76f8\u5bf9\u4f4e\u8868\u8fbe #\u7684\u6837\u672c\u88ab\u6807\u8bb0\u4e3a\u84dd\u8272\u3002\u6d45\u8272\u548c\u767d\u8272\u4ee3\u8868\u4e2d\u7b49\u8868\u8fbe\u6c34\u5e73\u7684\u57fa\u56e0\u3002\u6837\u672c\u548c\u57fa\u56e0\u5df2\u901a\u8fc7\u5206\u5c42\u805a\u7c7b\u7684 #\u65b9\u6cd5\u91cd\u65b0\u6392\u5e8f\u3002\u56fe\u4e2d\u8fd8\u663e\u793a\u6709\u6837\u672c\u805a\u7c7b\u7684\u6811\u72b6\u56fe\u3002<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.5727069351230425\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_hliaGcvFB2mhbPRnmIaT8CSWOFPibw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxkQdNGeWtDGfzAUzolwgtQMicRHOYK8huzSyicLPkQiceTUheEzhliaGcvFB2mhbPRnmIaT8CSWOFPibw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"447\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p><br \/><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><span style=\"font-size: 14px;\">\u4ee5\u4e0a\u5c31\u662f\u57fa\u56e0\u5dee\u5f02\u6027\u5206\u6790\u5e38\u7528\u7684<\/span>R<span style=\"font-size: 14px;\">\u5305\uff5e\u6b22\u8fce\u5927\u5bb6\u6765\u548c\u5c0f\u679c\u4ea4\u6d41\u54e6\uff01<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u8fd8\u6709\u66f4\u591a\u65b9\u4fbf\u5b9e\u7528\u7684\u5c0f\u5de5\u5177\u5728\u4e91\u751f\u4fe1\u5e73\u53f0\u7b49\u7740\u4f60\u54e6\uff5e<\/span><span style=\"text-align: center;letter-spacing: 0.034em;\"><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">http:\/\/www.biocloudservice.com\/home.html<\/span><span style=\"mso-spacerun:'yes';font-family:Calibri;mso-fareast-font-family:\u5b8b\u4f53;mso-bidi-font-family:'Times New 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sans-serif;\">\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(http:\/\/www.biocloudservice.com\/home.html)\uff0c\u5176\u4e2d\u4e5f\u5305\u62ec\u4e86\u901a\u8def\u8868\u8fbe\u5206\u6790(http:\/\/www.biocloudservice.com\/313\/313.php)\uff0c\u5355\u7ec6\u80de\u7684\u57fa\u56e0\u5171\u8868\u8fbe\u5206\u6790(http:\/\/www.biocloudservice.com\/906\/906.php)\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<\/span><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<section style=\"margin-bottom: 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\/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u57fa\u56e0\u5dee\u5f02\u6027\u5206\u6790\u4e09\u5927\u5229\u5668\u5927\u63ed\u79d8\uff0c\u8ba9\u4f60\u79d2\u61c2\u5982\u4f55\u9009\u62e9\uff01 \u539f\u521b \u5c0f\u679c \u751f\u4fe1 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{"id":54270,"date":"2024-06-16T13:49:48","date_gmt":"2024-06-16T05:49:48","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=54270"},"modified":"2024-06-16T13:49:48","modified_gmt":"2024-06-16T05:49:48","slug":"%e5%9f%ba%e5%9b%a0%e5%b7%ae%e5%bc%82%e6%80%a7%e5%88%86%e6%9e%90%e4%b8%89%e5%a4%a7%e5%88%a9%e5%99%a8%e5%a4%a7%e6%8f%ad%e7%a7%98%ef%bc%8c%e8%ae%a9%e4%bd%a0%e7%a7%92%e6%87%82%e5%a6%82%e4%bd%95%e9%80%89","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=54270","title":{"rendered":"\u57fa\u56e0\u5dee\u5f02\u6027\u5206\u6790\u4e09\u5927\u5229\u5668\u5927\u63ed\u79d8\uff0c\u8ba9\u4f60\u79d2\u61c2\u5982\u4f55\u9009\u62e9\uff01"},"content":{"rendered":"

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0.5px;\"><strong><span style=\"font-size: 15px;\">\u751f\u4fe1\u4ebaR\u8bed\u8a00\u5b66\u4e60\u5fc5\u5907<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u7acb\u523b\u62e5\u6709\u4e00\u4e2aRstudio\u8d26\u53f7<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u5f00\u542f\u5347\u7ea7\u6a21\u5f0f\u5427<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"color: rgb(255, 129, 36);font-size: 12px;letter-spacing: 0.5px;\">\uff0856\u7ebf\u7a0b\uff0c256G\u5185\u5b58\uff0c\u4e2a\u4eba\u5b58\u50a81T\uff09<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: 29.9652%;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 29.9652% 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data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<section style=\"display: contents;\" powered-by=\"xiumi.us\">\n<section style=\"display: contents;\">\n<section style=\"display: contents;\">\n<section style=\"height: 0px;overflow: hidden;\"><span style=\"font-size: 14px;letter-spacing: 0.578px;caret-color: red;\"> <\/span><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><span style=\"text-align: left;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\">\u57fa\u56e0\u6570\u636e\u7684\u5dee\u5f02\u6027\u5206\u6790\u662f\u4e00\u79cd\u9488\u5bf9\u4e0d\u540c\u751f\u7269\u6837\u672c\u6216\u4e0d\u540c\u5904\u7406\u6761\u4ef6\u4e0b\u57fa\u56e0\u8868\u8fbe\u91cf\u53d8\u5316\u7684\u5206\u6790\u65b9\u6cd5\u3002\u5b83\u53ef\u4ee5\u7528\u6765\u8bc6\u522b\u57fa\u56e0\u5728\u4e24\u4e2a\u6216\u591a\u4e2a\u6837\u672c\u4e4b\u95f4\u7684\u8868\u8fbe\u5dee\u5f02\uff0c\u4ece\u800c\u5e2e\u52a9\u6211\u4eec\u4e86\u89e3\u57fa\u56e0\u5728\u4e0d\u540c\u751f\u7269\u72b6\u6001\u4e0b\u7684\u529f\u80fd\u548c\u8c03\u63a7\u673a\u5236\u3002\u5bf9\u4e8e\u57fa\u56e0\u82af\u7247\u7684\u5dee\u5f02\u8868\u8fbe\u5206\u6790\uff0c\u7531\u4e8e\u5176\u6570\u636e\u666e\u904d\u88ab\u8ba4\u4e3a\u670d\u4ece\u6b63\u6001\u5206\u5e03\uff0c\u56e0\u6b64\u5e38\u7528\u7684\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u65b9\u6cd5\u662f\u5728\u6bcf\u4e2a\u57fa\u56e0\u4e0a\u5e94\u7528<\/span><span style=\"text-align: left;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\">t<\/span><span style=\"text-align: left;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\">\u68c0\u9a8c\u6216\u65b9\u5dee\u5206\u6790\u3002\u800c\u9ad8\u901a\u91cf\u5206\u6790\u6d89\u53ca\u5230\u591a\u4e2a\u57fa\u56e0\u7684\u540c\u65f6\u68c0\u9a8c\uff0c\u56e0\u6b64\u9700\u8981\u8fdb\u884c\u591a\u91cd\u6bd4\u8f83\u6821\u6b63\uff0c\u4ee5\u63a7\u5236\u5047\u9633\u6027\u7684\u53d1\u751f\u3002<\/span><br \/><\/p>\n<\/section>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u57fa\u56e0\u6570\u636e\u7684\u5dee\u5f02\u6027\u5206\u6790\u901a\u5e38\u5305\u62ec\u4ee5\u4e0b\u6b65\u9aa4\uff1a<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u6570\u636e\u9884\u5904\u7406\uff1a\u5305\u62ec\u5bf9\u539f\u59cb\u6570\u636e\u8fdb\u884c\u8d28\u91cf\u63a7\u5236\u3001\u53bb\u9664\u6389\u4f4e\u8d28\u91cf\u7684\u57fa\u56e0\u548c\u6837\u672c\u3001\u8fdb\u884c\u5f52\u4e00\u5316\u7b49\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><span style=\"font-size: 14px;\">\u5dee\u5f02\u6027\u5206\u6790\uff1a\u901a\u8fc7\u7edf\u8ba1\u5b66\u65b9\u6cd5\uff08\u5982<\/span>t<span style=\"font-size: 14px;\">\u68c0\u9a8c\u3001\u65b9\u5dee\u5206\u6790\u3001<\/span><span style=\"font-size: 14px;\">Wilcoxon<\/span><span style=\"font-size: 14px;\">\u68c0\u9a8c\u7b49\uff09\u6216\u673a\u5668\u5b66\u4e60\u65b9\u6cd5\uff08\u5982\u652f\u6301\u5411\u91cf\u673a\u3001\u968f\u673a\u68ee\u6797\u7b49\uff09\u6765\u6bd4\u8f83\u4e0d\u540c\u6837\u672c\u4e4b\u95f4\u7684\u57fa\u56e0\u8868\u8fbe\u91cf\uff0c\u627e\u51fa\u8868\u8fbe\u91cf\u663e\u8457\u5dee\u5f02\u7684\u57fa\u56e0\u3002\u5dee\u5f02\u6027\u5206\u6790\u7684\u7ed3\u679c\u53ef\u4ee5\u7528<\/span><span style=\"font-size: 14px;\">Volcano<\/span><span style=\"font-size: 14px;\">\u56fe\u6216<\/span><span style=\"font-size: 14px;\">Heatmap<\/span><span style=\"font-size: 14px;\">\u7b49\u65b9\u5f0f\u8fdb\u884c\u53ef\u89c6\u5316\u5c55\u793a\uff0c\u4ee5\u4fbf\u66f4\u597d\u5730\u7406\u89e3\u5dee\u5f02\u57fa\u56e0\u7684\u7279\u70b9\u548c\u8868\u8fbe\u6a21\u5f0f\u3002<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u529f\u80fd\u5bcc\u96c6\u5206\u6790\uff1a\u5bf9\u5dee\u5f02\u57fa\u56e0\u8fdb\u884c\u529f\u80fd\u5bcc\u96c6\u5206\u6790\uff0c\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u4e86\u89e3\u8fd9\u4e9b\u57fa\u56e0\u5728\u751f\u7269\u5b66\u8fc7\u7a0b\u3001\u901a\u8def\u3001\u529f\u80fd\u548c\u75be\u75c5\u4e2d\u7684\u4f5c\u7528\u548c\u8c03\u63a7\u673a\u5236\u3002\u529f\u80fd\u5bcc\u96c6\u5206\u6790\u65b9\u6cd5\u5305\u62ec\u57fa\u56e0\u672c\u4f53\u8bba\u5206\u6790\u3001\u5bcc\u96c6\u5206\u6790\u3001\u901a\u8def\u5206\u6790\u7b49\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u7ed3\u679c\u89e3\u91ca\u548c\u9a8c\u8bc1\uff1a\u57fa\u4e8e\u5dee\u5f02\u6027\u5206\u6790\u548c\u529f\u80fd\u5bcc\u96c6\u5206\u6790\u7684\u7ed3\u679c\uff0c\u53ef\u4ee5\u8fdb\u4e00\u6b65\u8fdb\u884c\u5b9e\u9a8c\u9a8c\u8bc1\uff0c\u4ee5\u786e\u5b9a\u5dee\u5f02\u57fa\u56e0\u7684\u751f\u7269\u5b66\u610f\u4e49\u548c\u529f\u80fd\uff0c\u4ece\u800c\u66f4\u597d\u5730\u7406\u89e3\u57fa\u56e0\u5728\u4e0d\u540c\u751f\u7269\u72b6\u6001\u4e0b\u7684\u4f5c\u7528\u548c\u8c03\u63a7\u673a\u5236\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">DESeq2<span style=\"font-size: 14px;\">\uff0c<\/span><span style=\"font-size: 14px;\">EdgeR<\/span><span style=\"font-size: 14px;\">\u548c<\/span><span style=\"font-size: 14px;\">limma<\/span><span style=\"font-size: 14px;\">\u662f\u4e09\u79cd<\/span><span style=\"font-size: 14px;\">R<\/span><span style=\"font-size: 14px;\">\u8bed\u8a00\u4e2d\u5e38\u7528\u7684\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u5de5\u5177\u5305\uff0c\u53ef\u4ee5\u7528\u4e8e\u5206\u6790<\/span><span style=\"font-size: 14px;\">RNA-seq<\/span><span style=\"font-size: 14px;\">\u6216<\/span><span style=\"font-size: 14px;\">microarray<\/span><span style=\"font-size: 14px;\">\u7b49\u9ad8\u901a\u91cf\u6570\u636e\u7684\u5dee\u5f02\u8868\u8fbe\u3002<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><span style=\"font-size: 14px;\"><br \/><\/span><\/span><\/p>\n<p><span style=\"text-decoration: underline;\"><strong><span style=\"text-decoration: underline;font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;color: rgb(61, 170, 214);\">DESeq2\uff1a<\/span><\/strong><\/span><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u4e00\u822c\u5dee\u5f02\u5206\u6790\u8f6f\u4ef6\u5982DESeq2\u548cedgeR\u7684\u539f\u7406\u662f\u6bd4\u8f83\u7ec4\u95f4\u5dee\u5f02\u548c\u7ec4\u5185\u5dee\u5f02\u3002\u6240\u4ee5\u8bf4\u901a\u5e38\u60c5\u51b5\u4e0b\uff0c\u5982\u679c\u6ca1\u6709\u91cd\u590d\uff0c\u5219\u7ec4\u5185\u5dee\u5f02\u65e0\u6cd5\u8ba1\u7b97\u3002DESeq2\u91c7\u7528\u6570\u636e\u5f52\u4e00\u5316\u548c\u53bb\u9664\u6279\u6b21\u6548\u5e94\u7684\u65b9\u6cd5\uff0c\u4ee5\u6d88\u9664\u6837\u672c\u4e4b\u95f4\u7684\u6280\u672f\u53d8\u5f02\u3002\u5b83\u901a\u8fc7\u5bf9\u6837\u672c\u4e2d\u7684\u57fa\u56e0\u8ba1\u6570\u6570\u636e\u8fdb\u884c\u8d1f\u4e8c\u9879\u5f0f\u6a21\u578b\u62df\u5408\uff0c\u6765\u9274\u5b9a\u57fa\u56e0\u5728\u4e0d\u540c\u6837\u672c\u4e4b\u95f4\u7684\u8868\u8fbe\u5dee\u5f02\u5e76\u8fdb\u884c\u5dee\u5f02\u57fa\u56e0\u7684\u7edf\u8ba1\u663e\u8457\u6027\u68c0\u9a8c\u3002\u540c\u65f6\u4e5f\u53ef\u7528\u4e8e\u8003\u8651\u751f\u7269\u5b66\u91cd\u590d\u7684\u5f71\u54cd\uff0c\u4ece\u800c\u66f4\u51c6\u786e\u5730\u4f30\u8ba1\u57fa\u56e0\u8868\u8fbe\u91cf\u7684\u65b9\u5dee\u548c\u6807\u51c6\u8bef\u5dee\u3002DESeq2\u4f7f\u7528Wald\u68c0\u9a8c\u6765\u9274\u5b9a\u5dee\u5f02\u57fa\u56e0\uff0c\u5e76\u4f7f\u7528Benjamini-Hochberg\u65b9\u6cd5\u6765\u8fdb\u884c\u591a\u91cd\u68c0\u9a8c\u6821\u6b63\u3002\u53e6\u5916\uff0cDESeq2\u8fd8\u63d0\u4f9b\u4e86\u591a\u79cd\u53ef\u89c6\u5316\u65b9\u6cd5\uff0c\u5982MA\u56fe\u3001Heatmap\u548cPCA\u5206\u6790\u7b49\u3002<\/span><\/p>\n<p><br \/><\/p>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<h1 style=\"text-align: center;\"><em style=\"letter-spacing: 0.034em;\"><\/em><\/h1>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"properties\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">##DESeq\u5dee\u5f02\u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attr\">dds<\/span> <span class=\"code-snippet__string\"><- estimateSizeFactors(dds) \u8ba1\u7b97\u5f52\u4e00\u5316\u7cfb\u6570sizeFactor<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attr\">dds<\/span> <span class=\"code-snippet__string\"><- estimateDispersions(dds) \u4f30\u8ba1\u57fa\u56e0\u7684\u79bb\u6563\u7a0b\u5ea6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attr\">dds <- nbinomWaldTest(dds) \u7edf\u8ba1\u68c0\u9a8c\uff0c\u5dee\u5f02\u5206\u6790<\/span><\/span><\/code><\/pre>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.7729941291585127\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_fbe9QCNicZ8pvexHphqjEM1kiaq9eg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxkQdNGeWtDGfzAUzolwgtQ6CVCxLmR3W3mIUWH61esJLY6mdfbe9QCNicZ8pvexHphqjEM1kiaq9eg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"511\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">EdgeR\uff1a\u9002\u7528\u4e8eRNA-seq\u548cmicroarray\u6570\u636e\u3002\u4f7f\u7528\u8d1f\u4e8c\u9879\u5f0f\u6a21\u578b\u6765\u5bf9\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u8fdb\u884c\u5efa\u6a21\uff0c\u4f7f\u7528TMM\uff08trimmed mean of M values\uff09\u65b9\u6cd5\u8fdb\u884c\u6570\u636e\u5f52\u4e00\u5316\u3002EdgeR\u4f7f\u7528exact test\u6216quasi-likelihood F-test\u6765\u8fdb\u884c\u5dee\u5f02\u5206\u6790\u3002\u540c\u65f6\uff0c\u5b83\u4e5f\u4f7f\u7528Benjamini-Hochberg\u65b9\u6cd5\u6765\u8fdb\u884c\u591a\u91cd\u68c0\u9a8c\u6821\u6b63\u3002edgeR\u6709\u4e00\u90e8\u5206\u529f\u80fd\u662f\u4f9d\u8d56\u4e8elimma\u5305\u3002<\/span><span style=\"mso-spacerun:'yes';font-family:Calibri;mso-fareast-font-family:\u5b8b\u4f53;mso-bidi-font-family:'Times New Roman';\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"white-space:pre-wrap;font-family: Consolas, "Liberation Mono", Menlo, Courier, monospace;font-size: 14px;background-color: rgb(250, 250, 250);color: rgb(51, 51, 51);letter-spacing: 0.034em;\">\u200d<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.7148936170212766\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_LWB3EVicnMW1xq61QlNgmULiawmJBg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxkQdNGeWtDGfzAUzolwgtQEhxibWUObuywxdueic35MOxicqyzpLWB3EVicnMW1xq61QlNgmULiawmJBg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"470\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">limma\uff1a\u76ee\u524d\u5728\u57fa\u56e0\u82af\u7247\u7684\u5206\u6790\u7528\u7684\u6700\u591a\u7684\u5c31\u662flimma\u3002\u867d\u7136\u5b83\u662f\u9488\u5bf9\u82af\u7247\u6570\u636e\u5f00\u53d1\u7684\uff0c\u4f46\u4e5f\u6709limma-voom\u53ef\u4ee5\u5206\u6790\u8f6c\u5f55\u7ec4\u6570\u636e\u3002\u5728\u5904\u7406RNA-Seq\u6570\u636e\u65f6\uff0craw read count\u5148\u88ab\u8f6c\u6210log2-counts-per-million (logCPM)\uff0c\u7136\u540e\u5bf9mean-variance\u5173\u7cfb\u5efa\u6a21\u3002limma\u4f7f\u7528\u7ebf\u6027\u6a21\u578b\u6765\u5206\u6790microarray\u548cRNA-seq\u6570\u636e\u3002\u901a\u8fc7\u7ecf\u9a8cBayes\u65b9\u6cd5\u6765\u8c03\u6574\u57fa\u56e0\u8868\u8fbe\u503c\uff0c\u4ee5\u63d0\u9ad8\u5dee\u5f02\u57fa\u56e0\u7684\u68c0\u6d4b\u80fd\u529b\uff0c\u5e76\u4f7f\u7528FDR\u63a7\u5236\u65b9\u6cd5\u8fdb\u884c\u591a\u91cd\u68c0\u9a8c\u6821\u6b63\u3002limma\u4e5f\u63d0\u4f9b\u4e86\u8bb8\u591a\u53ef\u89c6\u5316\u65b9\u6cd5\uff0c\u5982MA\u56fe\u3001Heatmap\u548cVolcano\u56fe\u7b49\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5c0f\u679c\u4ee5limma\u4e3a\u4f8b\uff0c\u5e26\u5927\u5bb6\u5b9e\u8df5\u4e00\u4e0b\u5427\uff5e<\/span><span style=\"mso-spacerun:'yes';font-family:Calibri;mso-fareast-font-family:\u5b8b\u4f53;mso-bidi-font-family:'Times New Roman';\"><o:p><\/o:p><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"properties\"><code><span class=\"code-snippet_outer\">design <- model.matrix(~0+group+lane)<\/span><\/code><code><span class=\"code-snippet_outer\">colnames(design) <- gsub(\"group\", \"\", colnames(design))<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">contr.matrix <- makeContrasts(<\/span><\/code><code><span class=\"code-snippet_outer\"> BasalvsLP = Basal-LP, <\/span><\/code><code><span class=\"code-snippet_outer\"> BasalvsML = Basal - ML, <\/span><\/code><code><span class=\"code-snippet_outer\"> LPvsML = LP - ML, <\/span><\/code><code><span class=\"code-snippet_outer\"> levels = colnames(design))<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">par(mfrow=c(1,2))<\/span><\/code><code><span class=\"code-snippet_outer\">v <- voom(x, design, plot=TRUE)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">vfit <- lmFit(v, design)<\/span><\/code><code><span class=\"code-snippet_outer\">vfit <- contrasts.fit(vfit, contrasts=contr.matrix)<\/span><\/code><code><span class=\"code-snippet_outer\">efit <- eBayes(vfit)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">summary(decideTests(efit))<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">tfit <- treat(vfit, lfc=1)<\/span><\/code><code><span class=\"code-snippet_outer\">dt <- decideTests(tfit)<\/span><\/code><code><span class=\"code-snippet_outer\">summary(dt)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">de.common <- which(dt[,1]!=0 & dt[,2]!=0)<\/span><\/code><code><span class=\"code-snippet_outer\">length(de.common)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">vennDiagram(dt[,1:2], circle.col=c(\"turquoise\", \"salmon\")<\/span><\/code><code><span class=\"code-snippet_outer\">#\u97e6\u6069\u56fe\u5c55\u793a\u4e86\u4ec5basal\u548cLP\uff08\u5de6\uff09\u3001\u4ec5basal\u548cML\uff08\u53f3\uff09\u7684\u5bf9\u6bd4\u7684DE\u57fa\u56e0\u6570\u91cf\uff0c\u8fd8\u6709\u4e24#\u79cd\u5bf9\u6bd4\u4e2d\u5171\u540c\u7684DE\u57fa\u56e0\u6570\u91cf\uff08\u4e2d\uff09\u3002\u5728\u4efb\u4f55\u5bf9\u6bd4\u4e2d\u5747\u4e0d\u5dee\u5f02\u8868\u8fbe\u7684\u57fa\u56e0\u6570\u91cf\u6807\u4e8e\u53f3\u4e0b\u3002<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><br \/><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.7923076923076923\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_N6L66N3rC0KYPfjJUPNLnZXfjWt2nw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxkQdNGeWtDGfzAUzolwgtQvddzpJ4xRRvaBHn3mMH0dCLVN6L66N3rC0KYPfjJUPNLnZXfjWt2nw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"390\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"bash\"><code><span class=\"code-snippet_outer\">library(gplots)<\/span><\/code><code><span class=\"code-snippet_outer\">basal.vs.lp.topgenes <- basal.vs.lp$ENTREZID[1:100]<\/span><\/code><code><span class=\"code-snippet_outer\">i <- which(v$genes$ENTREZID %in% basal.vs.lp.topgenes)<\/span><\/code><code><span class=\"code-snippet_outer\">mycol <- colorpanel(1000,\"blue\",\"white\",\"red\")<\/span><\/code><code><span class=\"code-snippet_outer\">heatmap.2(lcpm[i,], scale=\"row\",<\/span><\/code><code><span class=\"code-snippet_outer\"> labRow=v$genes$SYMBOL[i], labCol=group, <\/span><\/code><code><span class=\"code-snippet_outer\"> col=mycol, trace=\"none\", density.info=\"none\", <\/span><\/code><code><span class=\"code-snippet_outer\"> margin=c(8,6), lhei=c(2,10), dendrogram=\"column\"<\/span><\/code><code><span class=\"code-snippet_outer\"> #\u5728basal\u548cLP\u7684\u5bf9\u6bd4\u4e2d\u524d100\u4e2aDE\u57fa\u56e0log-CPM\u503c\u7684\u70ed\u56fe\u3002\u8c03\u6574\u540e\uff0c\u6bcf\u4e2a\u57fa\u56e0\uff08\u6bcf\u884c\uff09#\u7684\u8868\u8fbe\u5747\u503c\u4e3a0\uff0c\u5e76\u4e14\u6807\u51c6\u5dee\u4e3a1\u3002\u7ed9\u5b9a\u57fa\u56e0\u76f8\u5bf9\u9ad8\u8868\u8fbe\u7684\u6837\u672c\u88ab\u6807\u8bb0\u4e3a\u7ea2\u8272\uff0c\u76f8\u5bf9\u4f4e\u8868\u8fbe #\u7684\u6837\u672c\u88ab\u6807\u8bb0\u4e3a\u84dd\u8272\u3002\u6d45\u8272\u548c\u767d\u8272\u4ee3\u8868\u4e2d\u7b49\u8868\u8fbe\u6c34\u5e73\u7684\u57fa\u56e0\u3002\u6837\u672c\u548c\u57fa\u56e0\u5df2\u901a\u8fc7\u5206\u5c42\u805a\u7c7b\u7684 #\u65b9\u6cd5\u91cd\u65b0\u6392\u5e8f\u3002\u56fe\u4e2d\u8fd8\u663e\u793a\u6709\u6837\u672c\u805a\u7c7b\u7684\u6811\u72b6\u56fe\u3002<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.5727069351230425\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_hliaGcvFB2mhbPRnmIaT8CSWOFPibw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxkQdNGeWtDGfzAUzolwgtQMicRHOYK8huzSyicLPkQiceTUheEzhliaGcvFB2mhbPRnmIaT8CSWOFPibw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"447\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p><br \/><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><span style=\"font-size: 14px;\">\u4ee5\u4e0a\u5c31\u662f\u57fa\u56e0\u5dee\u5f02\u6027\u5206\u6790\u5e38\u7528\u7684<\/span>R<span style=\"font-size: 14px;\">\u5305\uff5e\u6b22\u8fce\u5927\u5bb6\u6765\u548c\u5c0f\u679c\u4ea4\u6d41\u54e6\uff01<\/span><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u8fd8\u6709\u66f4\u591a\u65b9\u4fbf\u5b9e\u7528\u7684\u5c0f\u5de5\u5177\u5728\u4e91\u751f\u4fe1\u5e73\u53f0\u7b49\u7740\u4f60\u54e6\uff5e<\/span><span style=\"text-align: center;letter-spacing: 0.034em;\"><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">http:\/\/www.biocloudservice.com\/home.html<\/span><span style=\"mso-spacerun:'yes';font-family:Calibri;mso-fareast-font-family:\u5b8b\u4f53;mso-bidi-font-family:'Times New Roman';\"><o:p><\/o:p><\/span><\/p>\n<p><br \/><\/p>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, 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