{"id":65493,"date":"2026-09-19T21:33:19","date_gmt":"2026-09-19T13:33:19","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=65493"},"modified":"2026-09-19T21:33:19","modified_gmt":"2026-09-19T13:33:19","slug":"rna-seq-deg-threshold-padj-log2fc-guide","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/rna-seq-deg-threshold-padj-log2fc-guide\/","title":{"rendered":"\u8f6c\u5f55\u7ec4\u5dee\u5f02\u57fa\u56e0\u600e\u4e48\u9009\u9608\u503c\uff1fpadj\u3001FDR \u4e0e log2FC \u4e00\u6b21\u8bb2\u6e05"},"content":{"rendered":"<p>\u62ff\u5230\u8f6c\u5f55\u7ec4\u5dee\u5f02\u5206\u6790\u7ed3\u679c\uff0c\u5f88\u591a\u4eba\u7b2c\u4e00\u6b65\u5c31\u5361\u4f4f\u4e86\uff1a<strong>P &lt; 0.05 \u8fd8\u662f padj &lt; 0.05\uff1f|log2FC| \u9009 1 \u8fd8\u662f 0.58\uff1f\u7b5b\u51fa\u6765\u53ea\u6709\u51e0\u5341\u4e2a\u57fa\u56e0\uff0c\u80fd\u4e0d\u80fd\u628a\u9608\u503c\u653e\u5bbd\uff1f<\/strong><\/p>\n<p>\u8fd9\u4e9b\u9009\u62e9\u4f1a\u5f71\u54cd\u540e\u7eed\u7684\u5bcc\u96c6\u5206\u6790\u3001\u5019\u9009\u57fa\u56e0\u7b5b\u9009\u548c\u5b9e\u9a8c\u9a8c\u8bc1\u3002\u4e0b\u9762\u4ee5<strong>\u6709\u751f\u7269\u5b66\u91cd\u590d\u7684 bulk RNA-seq \u7ec4\u95f4\u6bd4\u8f83<\/strong>\u4e3a\u4f8b\uff0c\u628a\u9608\u503c\u7684\u542b\u4e49\u3001\u9002\u7528\u573a\u666f\u548c\u5bb9\u6613\u8e29\u7684\u5751\u8bb2\u6e05\u695a\u3002<\/p>\n<h2>\u4e00\u3001\u8f6c\u5f55\u7ec4\u5dee\u5f02\u57fa\u56e0\u9608\u503c\u600e\u4e48\u9009\uff1f\u5148\u770b\u8fd9\u5f20\u8868<\/h2>\n<p>\u5982\u679c\u7814\u7a76\u76ee\u6807\u662f\u7b5b\u9009\u53d8\u5316\u8f83\u660e\u663e\u7684\u5019\u9009\u57fa\u56e0\uff0c<strong>padj &lt; 0.05 \u4e14 |log2FC| \u2265 1<\/strong>\u53ef\u4ee5\u4f5c\u4e3a\u5e38\u89c1\u7684\u5019\u9009\u5217\u8868\u7b5b\u9009\u8d77\u70b9\uff0c\u4f46\u5b83\u4e0d\u662f\u6240\u6709\u8bfe\u9898\u901a\u7528\u7684\u6807\u51c6\u3002\u4e0b\u9762\u662f\u4fbf\u4e8e\u5236\u5b9a\u65b9\u6848\u7684\u573a\u666f\u5efa\u8bae\uff0c\u5e94\u5728\u67e5\u770b\u76ee\u6807\u57fa\u56e0\u662f\u5426\u5165\u9009\u4e4b\u524d\u786e\u5b9a\u3002<\/p>\n<div style=\"overflow-x:auto\">\n<table>\n<thead>\n<tr>\n<th>\u7814\u7a76\u76ee\u7684<\/th>\n<th>\u53ef\u8003\u8651\u7684\u65b9\u6848<\/th>\n<th>\u9700\u8981\u6ce8\u610f<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td>\u7b5b\u9009\u53d8\u5316\u8f83\u660e\u663e\u7684\u5019\u9009\u57fa\u56e0<\/td>\n<td>padj &lt; 0.05\uff0c|log2FC| \u2265 1<\/td>\n<td>\u7ed3\u5408\u8868\u8fbe\u91cf\u3001\u91cd\u590d\u4e00\u81f4\u6027\u548c\u7814\u7a76\u76f8\u5173\u6027\u7ee7\u7eed\u7b5b\u9009<\/td>\n<\/tr>\n<tr>\n<td>\u5173\u6ce8\u8f83\u6e29\u548c\u3001\u4f46\u53ef\u80fd\u6709\u610f\u4e49\u7684\u53d8\u5316<\/td>\n<td>padj &lt; 0.05\uff0c|log2FC| \u2265 log2(1.5)\uff0c\u7ea6 0.585<\/td>\n<td>\u9700\u6709\u63a5\u53d7 1.5 \u500d\u53d8\u5316\u7684\u751f\u7269\u5b66\u7406\u7531\uff0c\u4e0d\u80fd\u53ea\u56e0\u57fa\u56e0\u5c11\u800c\u8c03\u6574<\/td>\n<\/tr>\n<tr>\n<td>\u63a2\u7d22\u6027\u7814\u7a76\uff0c\u540e\u7eed\u80fd\u505a\u72ec\u7acb\u9a8c\u8bc1<\/td>\n<td>\u53ef\u9884\u5148\u8bbe\u7f6e padj &lt; 0.10\uff0c\u5e76\u8bf4\u660e\u6548\u5e94\u91cf\u8981\u6c42<\/td>\n<td>\u660e\u786e\u6807\u6ce8\u4e3a\u63a2\u7d22\u7ed3\u679c\uff0c\u63a5\u53d7\u66f4\u9ad8\u7684\u5047\u53d1\u73b0\u98ce\u9669<\/td>\n<\/tr>\n<tr>\n<td>\u7814\u7a76\u901a\u8def\u6574\u4f53\u53d8\u5316<\/td>\n<td>\u53ef\u4f7f\u7528\u9002\u5408\u7684\u5168\u57fa\u56e0\u6392\u5e8f\u5f00\u5c55 GSEA<\/td>\n<td>\u4e0d\u5fc5\u5148\u7b5b\u51fa\u4e00\u6279\u663e\u8457\u5dee\u5f02\u57fa\u56e0\uff1b\u4ecd\u9700\u62a5\u544a\u901a\u8def\u5c42\u9762\u7684\u591a\u91cd\u68c0\u9a8c\u7ed3\u679c<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n<p><strong>\u9608\u503c\u670d\u52a1\u4e8e\u7814\u7a76\u95ee\u9898\uff0c\u4e0d\u80fd\u7528\u6765\u51d1\u51fa\u201c\u5408\u9002\u6570\u91cf\u201d\u7684\u57fa\u56e0\u3002<\/strong>\u82e5\u8981\u6b63\u5f0f\u68c0\u9a8c\u53d8\u5316\u662f\u5426\u8d85\u8fc7\u67d0\u4e2a\u500d\u6570\uff0c\u5e94\u4f7f\u7528\u4e0b\u6587\u4ecb\u7ecd\u7684\u6548\u5e94\u91cf\u9608\u503c\u68c0\u9a8c\uff1b\u5b83\u4e0e\u7ed3\u679c\u8868\u4e0a\u7684\u53cc\u6761\u4ef6\u7b5b\u9009\u6709\u6240\u533a\u522b\u3002<\/p>\n<h2>\u4e8c\u3001P \u503c\u3001padj \u548c FDR\uff0c\u5e94\u8be5\u770b\u54ea\u4e00\u5217\uff1f<\/h2>\n<p>\u8f6c\u5f55\u7ec4\u901a\u5e38\u540c\u65f6\u68c0\u9a8c\u6210\u5343\u4e0a\u4e07\u4e2a\u57fa\u56e0\u3002\u4ec5\u7528\u539f\u59cb P \u503c\u7b5b\u9009\uff0c\u4f1a\u9762\u4e34\u591a\u91cd\u68c0\u9a8c\u95ee\u9898\u3002\u56e0\u6b64\uff0c\u5224\u65ad\u5168\u8f6c\u5f55\u7ec4\u8303\u56f4\u7684\u7edf\u8ba1\u663e\u8457\u6027\u65f6\uff0c\u901a\u5e38\u4f18\u5148\u770b\u7ecf\u8fc7\u591a\u91cd\u68c0\u9a8c\u6821\u6b63\u7684\u7ed3\u679c\uff0c\u5e76\u6838\u5bf9\u6240\u7528\u65b9\u6cd5\u3002<\/p>\n<ul>\n<li><strong>P \u503c\uff1a<\/strong>\u5355\u4e2a\u68c0\u9a8c\u7684\u7edf\u8ba1\u7ed3\u679c\uff0c\u4e0d\u7b49\u4e8e\u201c\u8fd9\u4e2a\u57fa\u56e0\u662f\u5047\u9633\u6027\u7684\u6982\u7387\u201d\u3002<\/li>\n<li><strong>padj \/ FDR \u5217\uff1a<\/strong>\u5e38\u89c1\u6d41\u7a0b\u63d0\u4f9b\u7684\u6821\u6b63\u540e\u7ed3\u679c\uff0c\u5177\u4f53\u5b9a\u4e49\u4ee5\u8f6f\u4ef6\u8f93\u51fa\u4e3a\u51c6\u3002DESeq2 \u9ed8\u8ba4\u4f7f\u7528 BH \u6821\u6b63\u3002<\/li>\n<li><strong>FDR &lt; 0.05\uff1a<\/strong>\u5728\u76f8\u5e94\u7edf\u8ba1\u5047\u8bbe\u6210\u7acb\u65f6\uff0c\u63a7\u5236\u6240\u5224\u663e\u8457\u7ed3\u679c\u4e2d\u5047\u53d1\u73b0\u6bd4\u4f8b\u7684\u671f\u671b\uff1b\u4e0d\u662f\u4fdd\u8bc1\u672c\u6b21\u540d\u5355\u6070\u597d\u53ea\u6709 5% \u9519\u8bef\u3002<\/li>\n<\/ul>\n<p>BH \u65b9\u6cd5\u7684\u5b9a\u4e49\u53ef\u67e5\u9605 <a href=\"https:\/\/stat.ethz.ch\/R-manual\/R-devel\/library\/stats\/html\/p.adjust.html\" target=\"_blank\" rel=\"noopener noreferrer\">R \u5b98\u65b9\u591a\u91cd\u68c0\u9a8c\u6821\u6b63\u6587\u6863<\/a>\u3002\u7ed3\u679c\u8868\u82e5\u540c\u65f6\u6709 <code>pvalue<\/code> \u548c <code>padj<\/code>\uff0c\u4e0d\u8981\u56e0\u4e3a\u540e\u8005\u7b5b\u4e0d\u5230\u9884\u671f\u57fa\u56e0\uff0c\u5c31\u6084\u6084\u6362\u7528\u524d\u8005\u3002<\/p>\n<h2>\u4e09\u3001|log2FC| \u9009 1 \u8fd8\u662f 0.58\uff1f\u5148\u628a\u500d\u6570\u7b97\u5bf9<\/h2>\n<p>\u8bbe\u6bd4\u8f83\u65b9\u5411\u4e3a\u201c\u5904\u7406\u7ec4\u76f8\u5bf9\u5bf9\u7167\u7ec4\u201d\uff0clog2FC \u4e3a\u6b63\u8868\u793a\u4e0a\u8c03\uff0c\u4e3a\u8d1f\u8868\u793a\u4e0b\u8c03\u3002<strong>log2FC = 1 \u5bf9\u5e94 2 \u500d\uff0clog2FC = \u22121 \u5bf9\u5e94 0.5 \u500d\uff1b\u7ea6 \u00b10.585 \u5bf9\u5e94 1.5 \u500d\u6216\u5176\u5012\u6570\u3002<\/strong>\u5b9e\u9645\u8bbe\u7f6e 1.5 \u500d\u9608\u503c\u65f6\u5efa\u8bae\u4f7f\u7528 <code>log2(1.5)<\/code>\uff0c\u907f\u514d\u628a 0.58 \u5f53\u4f5c\u7cbe\u786e\u503c\u3002<\/p>\n<p>\u4e24\u500d\u53d8\u5316\u4fbf\u4e8e\u7406\u89e3\uff0c\u5374\u4e0d\u662f\u751f\u7269\u5b66\u610f\u4e49\u7684\u7edf\u4e00\u5206\u754c\u7ebf\u3002\u8c03\u63a7\u4fe1\u53f7\u53ef\u80fd\u8868\u73b0\u4e3a\u8f83\u5c0f\u4f46\u4e00\u81f4\u7684\u53d8\u5316\uff1b\u4f4e\u8868\u8fbe\u57fa\u56e0\u4e5f\u53ef\u80fd\u56e0\u4f30\u8ba1\u4e0d\u7a33\u5b9a\u800c\u51fa\u73b0\u5f88\u5927\u7684\u500d\u6570\u3002<strong>\u4e0d\u80fd\u628a\u201c\u500d\u6570\u5927\u201d\u76f4\u63a5\u7b49\u540c\u4e8e\u201c\u503c\u5f97\u505a\u5b9e\u9a8c\u201d\u3002<\/strong><\/p>\n<p>\u9009\u5019\u9009\u57fa\u56e0\u65f6\uff0c\u5efa\u8bae\u540c\u65f6\u770b\u5404\u6837\u672c\u8868\u8fbe\u5206\u5e03\u3001\u6548\u5e94\u91cf\u4f30\u8ba1\u7684\u7a33\u5b9a\u6027\u3001\u72ec\u7acb\u8bc1\u636e\u548c\u9a8c\u8bc1\u53ef\u884c\u6027\u3002DESeq2 \u7684\u6548\u5e94\u91cf\u6536\u7f29\u53ef\u7528\u4e8e\u6539\u5584\u6392\u5e8f\u548c\u5c55\u793a\uff0c\u76f8\u5173\u65b9\u6cd5\u89c1 <a href=\"https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC4302049\/\" target=\"_blank\" rel=\"noopener noreferrer\">DESeq2 \u539f\u59cb\u7814\u7a76<\/a>\u3002\u62a5\u544a\u4e2d\u5e94\u8bf4\u660e\u7b5b\u9009\u7528\u7684\u662f\u539f\u59cb\u4f30\u8ba1\u8fd8\u662f\u6536\u7f29\u540e\u7684\u4f30\u8ba1\u3002<\/p>\n<h2>\u56db\u3001\u5dee\u5f02\u57fa\u56e0\u592a\u5c11\u6216\u592a\u591a\uff0c\u5148\u68c0\u67e5\u4ec0\u4e48\uff1f<\/h2>\n<h3>\u5dee\u5f02\u57fa\u56e0\u592a\u5c11\uff1a\u5148\u5206\u6e05\u662f\u4fe1\u53f7\u5f31\uff0c\u8fd8\u662f\u5206\u6790\u6709\u95ee\u9898<\/h3>\n<ol>\n<li><strong>\u68c0\u67e5\u8f93\u5165\u548c\u5206\u7ec4\uff1a<\/strong>\u662f\u5426\u62ff\u5230\u4e86\u9002\u5408\u6240\u7528\u65b9\u6cd5\u7684\u8ba1\u6570\u6570\u636e\uff1f\u6837\u672c\u540d\u4e0e\u5206\u7ec4\u8868\u662f\u5426\u4e00\u4e00\u5bf9\u5e94\uff1f\u6bd4\u8f83\u65b9\u5411\u662f\u5426\u6b63\u786e\uff1f<\/li>\n<li><strong>\u68c0\u67e5\u6837\u672c\u8d28\u91cf\uff1a<\/strong>\u7ed3\u5408 PCA\u3001\u6837\u672c\u76f8\u5173\u6027\u548c\u539f\u59cb\u8d28\u63a7\u8bb0\u5f55\u5224\u65ad\u5f02\u5e38\uff0c\u4e0d\u80fd\u4e3a\u4e86\u8ba9\u7ed3\u679c\u663e\u8457\u800c\u5220\u9664\u6837\u672c\u3002<\/li>\n<li><strong>\u68c0\u67e5\u5b9e\u9a8c\u8bbe\u8ba1\uff1a<\/strong>\u914d\u5bf9\u4fe1\u606f\u3001\u6279\u6b21\u53ca\u91cd\u8981\u534f\u53d8\u91cf\u662f\u5426\u5408\u7406\u7eb3\u5165\u6a21\u578b\uff1f\u5982\u679c\u6279\u6b21\u4e0e\u5206\u7ec4\u5b8c\u5168\u91cd\u5408\uff0c\u5355\u9760\u7edf\u8ba1\u6821\u6b63\u65e0\u6cd5\u62c6\u5f00\u4e8c\u8005\u3002<\/li>\n<li><strong>\u68c0\u67e5\u7edf\u8ba1\u529f\u6548\uff1a<\/strong>\u6837\u672c\u5c11\u6216\u7ec4\u5185\u5dee\u5f02\u5927\u65f6\uff0c\u771f\u5b9e\u53d8\u5316\u4e5f\u53ef\u80fd\u672a\u8fbe\u5230\u663e\u8457\u3002\u6ca1\u6709\u663e\u8457\u5dee\u5f02\uff0c\u4e0d\u7b49\u4e8e\u8bc1\u660e\u6ca1\u6709\u751f\u7269\u5b66\u53d8\u5316\u3002<\/li>\n<\/ol>\n<p>\u751f\u7269\u5b66\u91cd\u590d\u5bf9\u68c0\u51fa\u80fd\u529b\u7684\u5f71\u54cd\u89c1 <a href=\"https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC4878611\/\" target=\"_blank\" rel=\"noopener noreferrer\">Schurch \u7b49\u4eba\u7684 RNA-seq \u91cd\u590d\u6570\u7814\u7a76<\/a>\u3002\u5177\u4f53\u6837\u672c\u91cf\u4ecd\u5e94\u7ed3\u5408\u7269\u79cd\u3001\u7ec4\u7ec7\u5f02\u8d28\u6027\u548c\u76ee\u6807\u6548\u5e94\u8bc4\u4f30\uff0c\u4e0d\u80fd\u7167\u642c\u4e00\u4e2a\u56fa\u5b9a\u6570\u5b57\u3002<\/p>\n<h3>\u5dee\u5f02\u57fa\u56e0\u592a\u591a\uff1a\u522b\u53ea\u60f3\u7740\u63d0\u9ad8\u9608\u503c<\/h3>\n<p>\u5f3a\u70c8\u5904\u7406\u6548\u5e94\u3001\u7ec4\u7ec7\u7ec4\u6210\u53d8\u5316\u6216\u6280\u672f\u56e0\u7d20\uff0c\u90fd\u53ef\u80fd\u4f7f\u5927\u91cf\u57fa\u56e0\u51fa\u73b0\u53d8\u5316\u3002\u5148\u786e\u8ba4\u8bbe\u8ba1\u548c\u6570\u636e\uff0c\u518d\u6309\u7814\u7a76\u95ee\u9898\u7f29\u5c0f\u5019\u9009\u8303\u56f4\u3002\u51c6\u5907\u6311\u9009\u9a8c\u8bc1\u57fa\u56e0\u65f6\uff0c\u53ef\u589e\u52a0\u72ec\u7acb\u961f\u5217\u4e00\u81f4\u6027\u3001\u901a\u8def\u5173\u8054\u548c\u5b9e\u9a8c\u53ef\u884c\u6027\u7b49\u8bc1\u636e\uff1b\u4e0d\u8981\u53ea\u4fdd\u7559\u6700\u5bb9\u6613\u8bb2\u6545\u4e8b\u7684\u4e00\u5c0f\u90e8\u5206\u3002<\/p>\n<p>\u53ef\u4ee5\u9884\u5148\u6bd4\u8f83\u51e0\u7ec4\u5408\u7406\u9608\u503c\u4e0b\u7684\u5019\u9009\u540d\u5355\u4e0e\u4e3b\u8981\u901a\u8def\uff0c\u4f5c\u4e3a<strong>\u654f\u611f\u6027\u5206\u6790<\/strong>\uff0c\u5e76\u8bb0\u5f55\u7ed3\u8bba\u662f\u5426\u7a33\u5b9a\u3002\u82e5\u4e00\u70b9\u70b9\u9608\u503c\u53d8\u5316\u5c31\u8ba9\u6838\u5fc3\u7ed3\u8bba\u7ffb\u8f6c\uff0c\u5e94\u5982\u5b9e\u8bf4\u660e\u8fd9\u79cd\u4e0d\u7a33\u5b9a\u6027\u3002<\/p>\n<blockquote>\n<p><strong>\u4f60\u4e5f\u9047\u5230\u4e86\u201c\u4e00\u4e2a\u57fa\u56e0\u90fd\u7b5b\u4e0d\u5230\u201d\u6216\u201c\u6362\u4e2a\u9608\u503c\u7ed3\u8bba\u5c31\u53d8\u201d\u7684\u60c5\u51b5\uff1f<\/strong><br \/>\u5148\u51c6\u5907\u6bcf\u7ec4\u6837\u672c\u6570\u3001\u662f\u5426\u914d\u5bf9\u3001\u5f53\u524d\u8f6f\u4ef6\u548c\u7b5b\u9009\u6761\u4ef6\u3002<a href=\"https:\/\/work.weixin.qq.com\/kfid\/kfcb05492f29d4d6064\" target=\"_blank\" rel=\"noopener noreferrer\" data-ysx-event=\"contact_click\">\u8054\u7cfb\u4e91\u751f\u4fe1\uff0c\u54a8\u8be2\u5dee\u5f02\u5206\u6790\u4e0e\u9608\u503c\u590d\u6838<\/a>\uff0c\u5148\u628a\u95ee\u9898\u5b9a\u4f4d\u6e05\u695a\uff0c\u518d\u8ba8\u8bba\u540e\u7eed\u5206\u6790\u8303\u56f4\u3002<\/p>\n<\/blockquote>\n<h2>\u4e94\u3001\u4e00\u4e2a\u5e38\u88ab\u5ffd\u7565\u7684\u533a\u522b\uff1a\u7b5b\u7ed3\u679c\u4e0e\u68c0\u9a8c\u500d\u6570\u9608\u503c<\/h2>\n<p><strong>\u201c\u5148\u68c0\u9a8c\u662f\u5426\u5b58\u5728\u53d8\u5316\uff0c\u518d\u7b5b\u9009 |log2FC| \u2265 1\u201d<\/strong>\u4e0e<strong>\u201c\u76f4\u63a5\u68c0\u9a8c\u771f\u5b9e\u53d8\u5316\u662f\u5426\u8d85\u8fc7\u4e24\u500d\u201d<\/strong>\u56de\u7b54\u7684\u662f\u4e0d\u540c\u95ee\u9898\u3002\u524d\u8005\u9002\u5408\u5f62\u6210\u5019\u9009\u5217\u8868\uff1b\u4e0d\u80fd\u636e\u6b64\u76f4\u63a5\u5ba3\u79f0\uff0c\u5217\u8868\u4e2d\u7684\u6bcf\u4e2a\u57fa\u56e0\u90fd\u5df2\u83b7\u5f97\u201c\u771f\u5b9e\u6548\u5e94\u8d85\u8fc7\u4e24\u500d\u201d\u7684\u7edf\u8ba1\u8bc1\u636e\uff0c\u4e5f\u4e0d\u80fd\u81ea\u52a8\u628a\u539f\u68c0\u9a8c\u7684 FDR \u4fdd\u8bc1\u5957\u5728\u4efb\u4f55\u4e8b\u540e\u7b5b\u9009\u7684\u5b50\u96c6\u4e0a\u3002<\/p>\n<p>\u82e5\u7814\u7a76\u95ee\u9898\u660e\u786e\u5173\u6ce8\u8d85\u8fc7\u67d0\u4e00\u6700\u5c0f\u6548\u5e94\u7684\u53d8\u5316\uff0c\u53ef\u91c7\u7528\u76f8\u5e94\u9608\u503c\u68c0\u9a8c\u3002\u8fd9\u4e2a\u601d\u8def\u89c1 <a href=\"https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC2654802\/\" target=\"_blank\" rel=\"noopener noreferrer\">TREAT \u65b9\u6cd5\u8bba\u6587<\/a>\uff1bedgeR \u53ef\u4f7f\u7528 <code>glmTreat()<\/code>\uff0c\u8be6\u89c1 <a href=\"https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC4934518\/\" target=\"_blank\" rel=\"noopener noreferrer\">edgeR \u5206\u6790\u6d41\u7a0b\u8bba\u6587<\/a>\u3002<\/p>\n<p>\u4e0b\u9762\u4ec5\u6f14\u793a\u4e24\u79cd\u7ed3\u679c\u63d0\u53d6\u65b9\u5f0f\u3002\u524d\u63d0\u662f <code>dds<\/code> \u5df2\u6309\u6b63\u786e\u8bbe\u8ba1\u5b8c\u6210 <code>DESeq()<\/code>\uff0c\u5206\u7ec4\u5217\u4e3a <code>condition<\/code>\uff0c\u6c34\u5e73\u786e\u5b9e\u4e3a <code>treated<\/code> \u4e0e <code>control<\/code>\uff1b\u4e0d\u80fd\u76f4\u63a5\u628a\u793a\u4f8b\u6807\u7b7e\u7167\u642c\u5230\u81ea\u5df1\u7684\u6570\u636e\u3002<\/p>\n<pre><code class=\"language-r\"># A. \u5e38\u89c1\u5019\u9009\u5217\u8868\uff1a\u96f6\u6548\u5e94\u68c0\u9a8c\u540e\uff0c\u518d\u6309\u4f30\u8ba1\u500d\u6570\u7b5b\u9009\nres &lt;- results(dds,\n  contrast = c(\"condition\", \"treated\", \"control\"), alpha = 0.05)\ndeg &lt;- res[which(!is.na(res$padj) &amp; res$padj &lt; 0.05 &amp;\n                 abs(res$log2FoldChange) &gt;= 1), ]\n\n# B. \u68c0\u9a8c\u771f\u5b9e\u6548\u5e94\u662f\u5426\u8d85\u8fc7\u4e24\u500d\uff0cP \u503c\u4f1a\u91cd\u65b0\u8ba1\u7b97\nres_effect &lt;- results(dds,\n  contrast = c(\"condition\", \"treated\", \"control\"),\n  alpha = 0.05, lfcThreshold = 1, altHypothesis = \"greaterAbs\")\ndeg_effect &lt;- res_effect[which(!is.na(res_effect$padj) &amp;\n                               res_effect$padj &lt; 0.05), ]<\/code><\/pre>\n<p>DESeq2 \u7684\u8f93\u5165\u3001\u8bbe\u8ba1\u3001<code>alpha<\/code> \u548c <code>lfcThreshold<\/code> \u8bf4\u660e\u89c1 <a href=\"https:\/\/bioconductor.org\/packages\/release\/bioc\/vignettes\/DESeq2\/inst\/doc\/DESeq2.html\" target=\"_blank\" rel=\"noopener noreferrer\">\u5b98\u65b9\u4f7f\u7528\u6587\u6863<\/a>\u3002\u4e0d\u8981\u628a TPM\/FPKM \u76f4\u63a5\u4f5c\u4e3a\u5e38\u89c4 DESeq2 \u8ba1\u6570\u77e9\u9635\u8f93\u5165\uff1b<code>padj = NA<\/code> \u4e5f\u4e0d\u7b49\u4e8e P \u503c\u4e3a 1\uff0c\u9700\u68c0\u67e5\u4f4e\u8ba1\u6570\u72ec\u7acb\u8fc7\u6ee4\u3001\u5168\u96f6\u8868\u8fbe\u6216\u5f02\u5e38\u503c\u7b49\u539f\u56e0\u3002<\/p>\n<h2>\u516d\u3001\u5dee\u5f02\u57fa\u56e0\u4e0d\u591a\uff0c\u8fd8\u80fd\u505a\u5bcc\u96c6\u5206\u6790\u5417\uff1f<\/h2>\n<p>\u5148\u533a\u5206\u4e24\u79cd\u5e38\u89c1\u5206\u6790\uff1a<strong>\u8fc7\u5ea6\u5bcc\u96c6\u5206\u6790\uff08ORA\uff09<\/strong>\u4ee5\u7b5b\u9009\u540e\u7684\u57fa\u56e0\u5217\u8868\u4e3a\u8f93\u5165\uff1b<strong>GSEA<\/strong>\u5173\u6ce8\u57fa\u56e0\u96c6\u5728\u6392\u5e8f\u4e2d\u7684\u6574\u4f53\u5206\u5e03\uff0c\u53ef\u4ee5\u4fdd\u7559\u672a\u8fbe\u5230\u5355\u57fa\u56e0\u663e\u8457\u6027\u9608\u503c\u7684\u4fe1\u53f7\u3002<\/p>\n<p>\u8fdb\u884c ORA \u65f6\uff0c\u5e94\u9009\u62e9\u4e0e\u68c0\u6d4b\u3001\u8fc7\u6ee4\u548c\u6ce8\u91ca\u8303\u56f4\u4e00\u81f4\u7684\u5408\u7406\u80cc\u666f\u57fa\u56e0\uff0c\u5e76\u8bf4\u660e\u662f\u5426\u5206\u522b\u5206\u6790\u4e0a\u8c03\u4e0e\u4e0b\u8c03\u57fa\u56e0\u3002\u505a GSEA \u65f6\uff0c\u4e0d\u8981\u53ea\u8f93\u5165\u5df2\u7b5b\u51fa\u7684\u663e\u8457\u57fa\u56e0\uff1b\u4f8b\u5982\u9488\u5bf9 DESeq2 \u7684\u4e24\u7ec4 Wald \u68c0\u9a8c\uff0c\u53ef\u4ee5\u4f7f\u7528\u5177\u6709\u65b9\u5411\u7684 Wald \u7edf\u8ba1\u91cf\u6392\u5e8f\uff0c\u5e76\u5904\u7406\u7f3a\u5931\u503c\u53ca\u91cd\u590d\u57fa\u56e0\u6807\u8bc6\u3002\u5177\u4f53\u8bbe\u7f6e\u53c2\u89c1 <a href=\"https:\/\/docs.gsea-msigdb.org\/GSEA\/GSEA_User_Guide\/\" target=\"_blank\" rel=\"noopener noreferrer\">GSEA \u5b98\u65b9\u6307\u5357<\/a>\u3002<\/p>\n<p>GSEA \u53ef\u4ee5\u5e2e\u52a9\u89c2\u5bdf\u5206\u6563\u4f46\u4e00\u81f4\u7684\u4fe1\u53f7\uff0c\u4f46\u4e0d\u80fd\u4fdd\u8bc1\u4e00\u5b9a\u4ea7\u751f\u663e\u8457\u901a\u8def\uff0c\u4e5f\u4e0d\u80fd\u4fee\u590d\u5206\u7ec4\u9519\u8bef\u3001\u6df7\u6742\u6216\u6837\u672c\u8d28\u91cf\u95ee\u9898\u3002\u4e0d\u8981\u4e3a\u5f97\u5230\u67d0\u6761\u9884\u671f\u901a\u8def\u800c\u53cd\u590d\u4fee\u6539\u9608\u503c\u3001\u80cc\u666f\u96c6\u548c\u57fa\u56e0\u96c6\u3002<\/p>\n<h2>\u4e03\u3001\u51c6\u5907\u9009\u57fa\u56e0\u505a\u9a8c\u8bc1\uff1f\u628a\u8fd9\u4e9b\u4fe1\u606f\u4e00\u8d77\u5e26\u4e0a<\/h2>\n<p>\u771f\u6b63\u5f71\u54cd\u540e\u7eed\u5b9e\u9a8c\u6295\u5165\u7684\uff0c\u662f\u5019\u9009\u662f\u5426\u53ef\u9760\u3001\u8bc1\u636e\u662f\u5426\u4e00\u81f4\u3001\u9a8c\u8bc1\u80fd\u5426\u56de\u7b54\u7814\u7a76\u95ee\u9898\u3002\u53ea\u6709\u4e00\u5f20\u706b\u5c71\u56fe\uff0c\u901a\u5e38\u4e0d\u8db3\u4ee5\u5224\u65ad\u3002<\/p>\n<p>\u54a8\u8be2\u65f6\u53ef\u4ee5\u76f4\u63a5\u590d\u5236\u4e0b\u9762\u8fd9\u4efd\u6e05\u5355\uff0c\u5148\u586b\u5199\u5df2\u6709\u4fe1\u606f\uff1a<\/p>\n<ul>\n<li><strong>\u7814\u7a76\u95ee\u9898\uff1a<\/strong>\u7269\u79cd\u3001\u7ec4\u7ec7\u6216\u7ec6\u80de\u7c7b\u578b\uff0c\u6700\u5e0c\u671b\u56de\u7b54\u4ec0\u4e48\u95ee\u9898\u3002<\/li>\n<li><strong>\u6837\u672c\u8bbe\u8ba1\uff1a<\/strong>\u5404\u7ec4\u6837\u672c\u6570\uff0c\u662f\u5426\u914d\u5bf9\uff0c\u662f\u5426\u5b58\u5728\u4e0d\u540c\u6279\u6b21\u3002<\/li>\n<li><strong>\u5df2\u6709\u6570\u636e\uff1a<\/strong>\u8ba1\u6570\u77e9\u9635\u3001\u5206\u7ec4\u8868\uff0c\u6216\u5305\u542b\u8868\u8fbe\u91cf\u3001log2FC\u3001P \u503c\u4e0e padj \u7684\u5b8c\u6574\u7ed3\u679c\u8868\u3002<\/li>\n<li><strong>\u5f53\u524d\u8bbe\u7f6e\uff1a<\/strong>\u5206\u6790\u8f6f\u4ef6\u3001\u6bd4\u8f83\u65b9\u5411\u3001\u9608\u503c\uff0c\u4ee5\u53ca\u76ee\u524d\u7b5b\u51fa\u7684\u57fa\u56e0\u6570\u91cf\u3002<\/li>\n<li><strong>\u4e0b\u4e00\u6b65\u76ee\u6807\uff1a<\/strong>\u5019\u9009\u57fa\u56e0\u9a8c\u8bc1\u3001\u901a\u8def\u89e3\u91ca\uff0c\u6216\u5df2\u6709\u5206\u6790\u7ed3\u679c\u590d\u6838\u3002<\/li>\n<\/ul>\n<p>\u4e91\u751f\u4fe1\u63d0\u4f9b<strong>\u8f6c\u5f55\u7ec4\u5206\u6790\u4e0e\u5b9a\u5236\u5206\u6790\u652f\u6301<\/strong>\u3002\u53ef\u4ee5\u56f4\u7ed5\u5206\u7ec4\u8bbe\u8ba1\u3001\u5dee\u5f02\u7ed3\u679c\u590d\u6838\u3001\u9608\u503c\u654f\u611f\u6027\u5206\u6790\u3001\u5bcc\u96c6\u89e3\u91ca\u548c\u5019\u9009\u57fa\u56e0\u4f18\u5148\u7ea7\u6c9f\u901a\u9700\u6c42\uff1b\u5177\u4f53\u670d\u52a1\u8303\u56f4\u3001\u4ea4\u4ed8\u5185\u5bb9\u3001\u5468\u671f\u4e0e\u8d39\u7528\uff0c\u5728\u4e86\u89e3\u6570\u636e\u540e\u786e\u8ba4\u3002<\/p>\n<p><a class=\"button\" href=\"https:\/\/work.weixin.qq.com\/kfid\/kfcb05492f29d4d6064\" target=\"_blank\" rel=\"noopener noreferrer\" data-ysx-event=\"contact_click\"><strong>\u54a8\u8be2\u8f6c\u5f55\u7ec4\u5206\u6790\uff5c\u53d1\u9001\u201c\u5dee\u5f02\u57fa\u56e0\u9608\u503c\u201d<\/strong><\/a><\/p>\n<p>\u5df2\u6709\u6570\u636e\u4f46\u4e0d\u786e\u5b9a\u4e0b\u4e00\u6b65\u600e\u4e48\u505a\uff0c\u53ef\u5148\u67e5\u770b<a href=\"https:\/\/www.biocloudservice.com\/wordpress\/services\/\" data-ysx-event=\"service_click\">\u4e91\u751f\u4fe1\u5206\u6790\u670d\u52a1<\/a>\uff1b\u4f7f\u7528\u516c\u5171\u6570\u636e\u7684\u8bfb\u8005\uff0c\u4e5f\u53ef\u4ee5\u7ee7\u7eed\u9605\u8bfb<a href=\"https:\/\/www.biocloudservice.com\/wordpress\/geo-data-mining-selection-validation-guide\/\">GEO \u6570\u636e\u6316\u6398\uff1a\u4ece\u6570\u636e\u7b5b\u9009\u5230\u7ed3\u679c\u9a8c\u8bc1<\/a>\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u8f6c\u5f55\u7ec4\u5dee\u5f02\u57fa\u56e0\u7528 P \u503c\u8fd8\u662f padj\uff1flog2FC \u9009 1 \u8fd8\u662f 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