{"id":57709,"date":"2024-06-16T20:26:47","date_gmt":"2024-06-16T12:26:47","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=57709"},"modified":"2026-09-11T23:07:49","modified_gmt":"2026-09-11T15:07:49","slug":"deseq2%e5%8c%85%e5%81%9a%e5%b7%ae%e5%bc%82%e5%88%86%e6%9e%90%ef%bc%8c%e7%ae%80%e5%8d%95%e6%98%93%e6%87%82%ef%bc%8c%e6%9c%89%e6%89%8b%e5%b0%b1%e8%a1%8c%ef%bc%8c%e4%bd%a0%e8%bf%98%e4%b8%8d%e5%ad%a6","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/deseq2%e5%8c%85%e5%81%9a%e5%b7%ae%e5%bc%82%e5%88%86%e6%9e%90%ef%bc%8c%e7%ae%80%e5%8d%95%e6%98%93%e6%87%82%ef%bc%8c%e6%9c%89%e6%89%8b%e5%b0%b1%e8%a1%8c%ef%bc%8c%e4%bd%a0%e8%bf%98%e4%b8%8d%e5%ad%a6\/","title":{"rendered":"DESeq2\u5305\u505a\u5dee\u5f02\u5206\u6790\uff0c\u7b80\u5355\u6613\u61c2\uff0c\u6709\u624b\u5c31\u884c\uff0c\u4f60\u8fd8\u4e0d\u5b66\uff1f"},"content":{"rendered":"<aside class=\"ysx-source-note\"><span>\u6765\u6e90<\/span><\/p>\n<p>\u516c\u4f17\u53f7\u300cR\u8bed\u8a00\u5b66\u5f92\u300d\u5386\u53f2\u5185\u5bb9\uff1b\u672c\u6587\u4fdd\u7559\u539f\u6709\u6280\u672f\u4fe1\u606f\u5e76\u4f18\u5316\u7f51\u9875\u6392\u7248\u3002 <a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg5MDk3Mzg4OA==&amp;mid=2247484311&amp;idx=1&amp;sn=2c95ff1a6ddc3d0545ece0a634909d04\" target=\"_blank\" rel=\"noopener noreferrer nofollow\">\u67e5\u770b\u539f\u6587<\/a><\/p>\n<\/aside>\n<p>\u8f6c\u5f55\u7ec4\u7684\u4e3b\u8981\u76ee\u7684\u4e4b\u4e00\u4fbf\u662f\u5bfb\u627e\u57fa\u56e0\u8868\u8fbe\u7684\u5dee\u5f02\u89e3\u91ca\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\u7684\u53d8\u5316\u5bf9\u751f\u7269\u529f\u80fd\u7684\u5f71\u54cd\u3002\u4f8b\u5982\uff0c\u5728\u764c\u53d8\u548c\u5176\u4ed6\u590d\u6742\u75be\u75c5\u53d1\u751f\u548c\u53d1\u5c55\u8fc7\u7a0b\u4e2d\uff0c\u7ec6\u80de\u5185\u7684\u57fa\u56e0\u8868\u8fbe\u6a21\u5f0f\u4f1a\u53d1\u751f\u663e\u8457\u6539\u53d8\u3002\u5728\u7ec6\u83cc\u548c\u75c5\u6bd2\u4fb5\u67d3\u65f6\uff0c\u7ec6\u80de\u5185\u7684\u57fa\u56e0\u8868\u8fbe\u6a21\u5f0f\u4e5f\u4f1a\u53d1\u751f\u663e\u8457\u53d8\u5316\uff0c\u8fd9\u4e9b\u53d8\u5316\u5bf9\u673a\u4f53\u7684\u6297\u611f\u67d3\u529f\u80fd\u81f3\u5173\u91cd\u8981\u3002\u5728\u690d\u7269\u7684\u6b63\u5e38\u751f\u957f\uff0c\u6297\u65f1\u3001\u6297\u9006\u3001\u4ee5\u53ca\u4f18\u826f\u54c1\u7cfb\u57f9\u80b2\u7b49\u8fc7\u7a0b\u4e2d\u7ec6\u80de\u7684\u57fa\u56e0\u8868\u8fbe\u6a21\u5f0f\u4f1a\u53d1\u751f\u663e\u8457\u53d8\u5316\u3002<\/p>\n<p>\u90a3\u4e48\uff0c\u5982\u4f55\u57fa\u4e8e\u8f6c\u5f55\u7ec4\u6d4b\u5e8f\u83b7\u5f97\u7684\u5b9a\u91cf\u8868\u8fbe\u503c\uff0c\u8bc6\u522b\u5dee\u5f02\u8868\u8fbe\u53d8\u5316\u7684\u57fa\u56e0\u6216\u5176\u5b83\u975e\u7f16\u7801RNA\u5206\u5b50\u5462\uff1f<\/p>\n<p>\u8f6c\u5f55\u7ec4\u6d4b\u5e8f\u5b8c\u6210\u540e\uff0c\u4e00\u822c\u6211\u4eec\u4f1a\u83b7\u5f97\u4e00\u4e2a\u539f\u59cb read count\u8868\u8fbe\u77e9\u9635\uff0c\u5176\u4e2d\u884c\u662f\u57fa\u56e0\uff0c\u5217\u662f\u6837\u54c1\u3002\u5e38\u7528\u7684\u5dee\u5f02\u5206\u6790\u5de5\u5177\u5305\u62eclimma\uff0cedgeR\uff0cDESeq2\u3002\u5c0f\u5e08\u59b9\u5c31\u4ee5R\u5305DESeq2\u7684\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\u5206\u6790\u65b9\u6cd5\u4e3a\u4f8b\u505a\u4e2a\u7b80\u5355\u6f14\u793a\uff0c\u8fd9\u662f\u76ee\u524d\u4f7f\u7528\u9891\u7387\u6700\u9ad8\u7684\u9274\u5b9a\u5dee\u5f02\u5206\u5b50\u7684R\u5305\u4e4b\u4e00\u3002<\/p>\n<p>\u7b80\u5355\u5730\u8bf4\uff0cDESeq2\u5c06\u5bf9\u539f\u59cbreads count\u8fdb\u884c\u5efa\u6a21\uff0c\u4f7f\u7528\u6807\u51c6\u5316\u56e0\u5b50\uff08scale factor\uff09\u6765\u89e3\u91ca\u5e93\u6df1\u5ea6\u7684\u5dee\u5f02\u3002\u7136\u540eDESeq2\u4f30\u8ba1\u57fa\u56e0\u7684\u79bb\u6563\u5ea6\uff0c\u5e76\u7f29\u5c0f\u8fd9\u4e9b\u4f30\u8ba1\u503c\u4ee5\u751f\u6210\u66f4\u51c6\u786e\u7684\u79bb\u6563\u5ea6\u4f30\u8ba1\uff0c\u4ece\u800c\u5bf9reads count\u8fdb\u884c\u5efa\u6a21\u3002\u6700\u540e\uff0cDESeq2\u62df\u5408\u8d1f\u4e8c\u9879\u5206\u5e03\u7684\u6a21\u578b\uff0c\u5e76\u4f7f\u7528Wald\u68c0\u9a8c\u6216\u4f3c\u7136\u6bd4\u68c0\u9a8c\u8fdb\u884c\u5047\u8bbe\u68c0\u9a8c\u3002<\/p>\n<p>\u53ea\u9700\u8981\u77e5\u9053\u600e\u4e48\u8dd1\uff0c\u51c6\u5907\u6570\u636e\uff0c\u4fee\u6539\u6570\u636e\u53c2\u6570\u5c31ok\u4e86\uff01<\/p>\n<p>\u8fd9\u91cc\u5c0f\u5e08\u59b9\u5c31\u4e0d\u8fc7\u591a\u4ecb\u7ecd\u8fd9\u4e2a\u5305\u5566\uff0c\u4e3b\u8981\u662f\u4ee5\u51fa\u7ed3\u679c\u4e3a\u76ee\u7684\u3002<\/p>\n<p>\u6240\u4ee5\u76f4\u63a5\u4e0a\u4ee3\u7801<\/p>\n<h2>1. \u5b89\u88c5\u5e76\u52a0\u8f7d DESeq2<\/h2>\n<p>install.packages(&#8216;BiocManager&#8217;) #\u9700\u8981\u9996\u5148\u5b89\u88c5 BiocManager\uff0c\u5982\u679c\u5c1a\u672a\u5b89\u88c5\u8bf7<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>install.packages('BiocManager') <\/code><code>#\u9700\u8981\u9996\u5148\u5b89\u88c5 BiocManager\uff0c\u5982\u679c\u5c1a\u672a\u5b89\u88c5\u8bf7\u5148\u6267\u884c\u8be5\u6b65<\/code><code>BiocManager::install('DESeq2')<\/code><code>library(\"DESeq2\")<\/code><code>#\u6d4b\u8bd5\u662f\u5426\u5b89\u88c5\u6210\u529f<\/code><\/pre>\n<\/div>\n<h2>2. \u51c6\u5907 count \u77e9\u9635\u4e0e\u5206\u7ec4<\/h2>\n<p>\u8fd9\u91cc\u51c6\u5907counts\u6587\u4ef6\u5373\u53ef<\/p>\n<p>\u201cmRNA_count.txt\u201d\uff0c\u662f6\u4e2a\u6d4b\u5e8f\u6837\u672c\u7684\u57fa\u56e0\u8868\u8fbe\u503c\u77e9\u9635\uff0c\u5305\u62ec3\u4e2a\u5904\u7406\u7ec4\uff08treat\uff09\u548c3\u4e2a\u5bf9\u7167\u7ec4\uff08control\uff09\u3002\u7b2c1\u5217\u662f\u57fa\u56e0\u540d\u79f0\uff0c\u6ce8\u610f\u4e0d\u80fd\u6709\u91cd\u590d\u503c\u3002<\/p>\n<figure><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_mxiaEXObF0ia4FjvXo8suicbfFPvOw.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/figure>\n<h2>3. \u6784\u5efa DESeq2 \u6570\u636e\u5bf9\u8c61<\/h2>\n<p>\u7136\u540e\u5c06\u51c6\u5907\u597d\u7684\u57fa\u56e0\u8868\u8fbe\u503c\u77e9\u9635\u8bfb\u5230R\u4e2d\uff0c\u5e76\u9884\u5b9a\u4e49\u6837\u672c\u5206\u7ec4\u4fe1\u606f<\/p>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>result=read.table(\"mRNA_count.txt\",header=T,seq=\u201dt\u201d,check.names=F) #\u8bfb\u53d6\u57fa\u56e0\u8868\u8fbe\u77e9\u9635<\/code><code>rownames(result)=result[,1]<\/code><code>result &lt;- result [which(rowSums(result) &gt; 0),]#\u6570\u636e\u9884\u5904\u7406\uff0c\u53bb\u9664\u5728\u5168\u90e8\u6837\u672c\u7686\u8868\u8fbe\u4e3a0\u7684\u57fa\u56e0<\/code><code>group_list &lt;- c(rep(\"control\",times = 3),rep(\"treat\",times = 3))#\u6307\u5b9a\u6837\u672c\u5206\u7ec4<\/code><code>exprSet=result<\/code><\/pre>\n<\/div>\n<h2>4. \u8fdb\u884c\u5dee\u5f02\u5206\u6790<\/h2>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>coldata &lt;- data.frame(row.names = colnames(exprSet),group_list=group_list) #\u6bcf\u4e00\u884c\u5bf9\u5e94\u4e00\u4e2a\u6837\u672c\uff0c\u884c\u540d\u4e0ecountData\u7684\u6837\u672c\u987a\u5e8f\u4e00\u4e00\u5bf9\u5e94\uff0c\u5217\u4e3a\u5404\u79cd\u5206\u7ec4\u4fe1\u606f\u3002<\/code><code>dds&lt;-DESeqDataSetFromMatrix(countData=exprSet,colData=coldata,design=~group_list) #\u6784\u5efaDESeqDataSet\u5bf9\u8c61<\/code><code>dds&lt;-DESeq(dds) #\u6807\u51c6\u5316<\/code><code>res&lt;-results(dds)#\u5c06\u7ed3\u679c\u7528results()\u51fd\u6570\u6765\u83b7\u53d6\uff0c\u8d4b\u503c\u7ed9res\u53d8\u91cf<\/code><code>class(res)#\u67e5\u770bres\u6570\u636e\u7c7b\u578b<\/code><code>res&lt;-as.data.frame(res) #\u7528data.frame\u8f6c\u5316res\u683c\u5f0f\u4e3a\u8868\u683c\u5f62\u5f0f<\/code><code>res&lt;-cbind(rownames(res),res) \u00a0<\/code><code>head(res)#\u67e5\u770b\u6784\u5efa\u597d\u7684\u8868\u8fbe\u77e9\u9635<\/code><code><br><\/code><code>res &lt;- results(dds,contrast = c(\"group_list\",\"treat\",\"control\"))#\u67e5\u770b\u57fa\u56e0\u7684\u5dee\u5f02\u500d\u6570\uff0c\u548c\u663e\u8457\u6027p\u503c\u3002treat\u5728\u524d\uff0ccontrol\u5728\u540e\uff0c\u610f\u4e3atreat\u76f8\u8f83\u4e8econtrol\u4e2d\u54ea\u4e9b\u57fa\u56e0\u4e0a\u8c03\/\u4e0b\u8c03\u3002<\/code><code>res0rdered &lt;- res[order(res$padj),]#\u5bf9p\u503c\u91cd\u65b0\u8fdb\u884c\u6392\u5e8f<\/code><code>head(res0rdered)#\u67e5\u770bres0rdered<\/code><code>DEG=as.data.frame(res0rdered)<\/code><code>DEG &lt;- na.omit(DEG)# \u53bb\u9664\u7f3a\u5931\u503cNA<\/code><code>DEG&lt;-cbind(rownames(DEG),DEG) <\/code><code>head(DEG)<\/code><code>colnames(res)&lt;-c('gene_id',\"baseMean\" ,\"log2FoldChange\",\"lfcSE\" ,\"stat\",\"pvalue\",\"padj\" )#res\u4e2d\uff0c\u5305\u542b\u4e86\u57fa\u56e0id\u3001\u6807\u51c6\u5316\u540e\u7684\u57fa\u56e0\u8868\u8fbe\u503c\uff08baseMean\uff09\u3001log2\u8f6c\u5316\u540e\u7684\u5dee\u5f02\u500d\u6570\uff08Fold Change\uff09\u503c\u3001\u663e\u8457\u6027p\u503c\u4ee5\u53ca\u6821\u6b63\u540ep\u503c\uff08\u9ed8\u8ba4FDR\u6821\u6b63\uff09\u7b49\u4e3b\u8981\u4fe1\u606f\u3002<\/code><code>write.table(res,\"control-mRNA.xls\",sep = 't',col.names = T,row.names = F,quote = FALSE,na='')#\u6587\u4ef6\u4fdd\u5b58\uff0c\u5f97\u5230\u5b8c\u6574\u8868\u683c<\/code><\/pre>\n<\/div>\n<h2>5. \u7b5b\u9009\u5e76\u5bfc\u51fa\u5dee\u5f02\u57fa\u56e0<\/h2>\n<div class=\"code-card\">\n<div class=\"code-head\"><span>\u4ee3\u7801<\/span><\/div>\n<pre><code>#\u83b7\u53d6padj\uff08p\u503c\u7ecf\u8fc7\u591a\u91cd\u6821\u9a8c\u6821\u6b63\u540e\u7684\u503c\uff09\u5c0f\u4e8e0.05\uff0c\u8868\u8fbe\u500d\u6570\u53d6\u4ee52\u4e3a\u5bf9\u6570\u540e\u5927\u4e8e1\u6216\u8005\u5c0f\u4e8e-1\u7684\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\u3002<\/code><code>resSig&lt;-res[which(res$padj&lt;0.05 &amp; abs(res$log2FoldChange&gt;1)),]<\/code><code>resSig[which(resSig$log2FoldChange&gt;0),'up_down']&lt;-'up'#\u8868\u8fbe\u91cf\u663e\u8457\u4e0a\u8c03\u7684\u57fa\u56e0<\/code><code>resSig[which(resSig$log2FoldChange&lt;0),'up_down']&lt;-'down'#\u8868\u8fbe\u91cf\u663e\u8457\u4e0b\u8c03\u7684\u57fa\u56e0<\/code><code>head(resSig)<\/code><code>write.table(resSig,\"control-mRNA-0.05.xls\",sep='t',col.names=T,row.names=F,quote = FALSE,na='')# \u8f93\u51fa\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u7ed3\u679c<\/code><\/pre>\n<\/div>\n<figure><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_icwhNbTHqMibHNSwKKAe7pBD8vm43g.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/figure>\n<p><strong>\u521d\u5b66\u8005\u6700\u597d\u5148\u6309\u7167\u8fd9\u4e2a\u65b9\u6cd5\u4e00\u6b65\u4e00\u6b65\u8d70\uff0c\u5305\u62ec\u547d\u540d\u3002\u6bcf\u4e00\u6b65\u51fa\u7ed3\u679c\u90fd\u67e5\u770b\u4e00\u4e0b\uff0c\u5982\u6b64\u4fbf\u4f1a\u987a\u5229\u4e9b\u5466\uff01<\/strong><\/p>\n<p>\u597d\u4e86\u5c0f\u5e08\u59b9\u4eca\u5929\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u5566\uff0c\u5c0f\u4f19\u4f34\u4eec\u6709\u9047\u5230\u95ee\u9898\u6b22\u8fce\u968f\u65f6\u6765\u627e\u5c0f\u5e08\u59b9\u5206\u4eab\u8ba8\u8bba\u5440\uff01<\/p>\n","protected":false},"excerpt":{"rendered":"<p>DESeq2\u5305\u505a\u5dee\u5f02\u5206\u6790\uff0c\u7b80\u5355\u6613\u61c2\uff0c\u6709\u624b\u5c31\u884c\uff0c\u4f60\u8fd8\u4e0d\u5b66\uff1f \u5c0f\u5e08\u59b9 \u751f\u4fe1\u679c 2023-07-05 19:00:29 \u8f6c\u81ea\u516c\u4f17\u53f7\uff1aR\u8bed\u8a00\u5b66\u5f92http:\/\/mp.weixin.qq.com\/s?__biz=Mzg5MDk3Mzg4OA==&#038;mid=2247484311\u2026<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_feature_clip_id":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_post_was_ever_published":false},"categories":[1,72],"tags":[],"class_list":["post-57709","post","type-post","status-publish","format-standard","hentry","category-part","category-transcriptomics"],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"","_links":{"self":[{"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/posts\/57709","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/comments?post=57709"}],"version-history":[{"count":2,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/posts\/57709\/revisions"}],"predecessor-version":[{"id":65421,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/posts\/57709\/revisions\/65421"}],"wp:attachment":[{"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/media?parent=57709"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/categories?post=57709"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/tags?post=57709"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}