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\u6570\u636e\u5e93\u4e0b\u8f7d\uff0c\u53ef\u4ee5\u76f4\u63a5\u8f93\u5165\u60f3\u67e5\u8be2\u7684\u75be\u75c5\u540d\u79f0\u5c31\u53ef\u4ee5\u8fdb\u884c\u641c\u7d22\u83b7\u5f97\u76f8\u5e94\u7684\u6570\u636e\uff0c\u7f51\u5740\u4e3a\uff1ahttps:\/\/www.ncbi.nlm.nih.gov\/gds\/?term=GSE70494<\/span><span style=\"text-align: center;letter-spacing: 0.578px;\"><\/span><\/p>\n<p><span style=\"font-size: 14px;\"><\/span><span style=\"text-align: center;letter-spacing: 0.578px;\"><\/span><\/p>\n<p><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.34115523465703973\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-19_\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790\/2_OrxV1uoibMnIZZvVPibrLGkHraZLqQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgYQVVs6ZbiaDDfvynk5TeGeuXibIbOrxV1uoibMnIZZvVPibrLGkHraZLqQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\"><\/p>\n<p><span style=\"font-size: 14px;\"><\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u7b2c\u4e8c\u79cd\u65b9\u6cd5\u662f\u901a\u8fc7\u4ee5\u53d1\u8868\u7684\u6587\u732e\u6765\u67e5\u8be2\u76f8\u5173\u75be\u75c5\u7684GEO ID\uff0c\u5c0f\u679c\u662f\u901a\u8fc7PubMed\u6765\u67e5\u8be2\uff0c\u53ea\u9700\u8981\u8f93\u5165\u76f8\u5173\u75be\u75c5\u5173\u952e\u5b57\u548cGEO\u5c31\u53ef\u4ee5\u641c\u7d22\u5230\u76f8\u5173\u6587\u7ae0\u548cGEO ID\uff0c\u8be5\u7f51\u5740\u4e3a\uff1ahttps:\/\/pubmed.ncbi.nlm.nih.gov\/?term=gene+family<\/span><\/p>\n<p><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.29061371841155237\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_XHNopzS3fxdE77iccYfEYicAS9Ne7g.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgCxWWQsZJuxHmhiaSsM69qx9PCxiaXHNopzS3fxdE77iccYfEYicAS9Ne7g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" data-recalc-dims=\"1\"><\/p>\n<p><span style=\"font-size: 14px;\"><\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u4e00\u822c\u901a\u8fc7\u8fd9\u4e24\u79cd\u65b9\u6cd5\u5c31\u53ef\u4ee5\u83b7\u53d6\u81ea\u5df1\u60f3\u8981\u7684GEO ID\uff0c\u901a\u8fc7\u5c0f\u679c\u7684\u65b9\u6cd5\u83b7\u5f97ID\u540e\uff0c\u5c31\u53ef\u4ee5\u8ddf\u7740\u5c0f\u679c\u5f00\u59cb\u4eca\u5929\u7684\u5b9e\u64cd\u5206\u6790\u5566\uff0c\u5176\u5b9e\u5c31\u662f\u8fd9\u4e48\u7b80\u5355\uff01\uff01\uff01\u54c8\u54c8\u54c8\u54c8\u54c8\u3002\u3002\u3002\u3002\u3002\u3002\u3002\u3002<\/span><\/p>\n<p><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;letter-spacing: 0.578px;font-size: 16px;margin-bottom: 0px;white-space: normal;\"><span style=\"font-size: 14px;\"><strong style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;white-space: normal;\"><em><span style=\"font-size: 20px;\">2. \u5bfc\u5165\u9700\u8981\u7684R\u5305<\/span><\/em><\/strong><\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">library(GEOquery)<\/span><\/code><code><span class=\"code-snippet_outer\">library(limma)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<p powered-by=\"xiumi.us\" style=\"text-align: center;letter-spacing: 0.578px;font-size: 16px;margin-bottom: 0px;white-space: normal;\"><span style=\"font-size: 14px;\"><strong style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;white-space: normal;\"><em><span style=\"font-size: 20px;\">3. \u4eceGEO\u4e0b\u8f7d\u8868\u8fbe\u77e9\u9635\u548c\u82af\u7247\u6ce8\u91ca\u6ce8\u91ca\u6587\u4ef6<\/span><\/em><\/strong><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">GSEdata <- getGEO(<span class=\"code-snippet__string\">\"GSE17215\"<\/span>, GSEMatrix=T, AnnotGPL=FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">eset <- GSEdata[[<span class=\"code-snippet__number\">1<\/span>]]<\/span><\/code><code><span class=\"code-snippet_outer\">#\u63d0\u53d6\u8868\u8fbe\u77e9\u9635,\u901a\u8fc7exprs\u51fd\u6570\u63d0\u53d6\uff0c\u884c\u540d\u4e3a\u63a2\u9488ID\uff0c\u5217\u540d\u4e3a\u6837\u672c\u540d<\/span><\/code><code><span class=\"code-snippet_outer\">exprSet <- as.data.frame(exprs(eset))<\/span><\/code><\/pre>\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=\"0.18592057761732853\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-19_\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790\/4_vh9OgKCUhNmHucOts4fL3WxIy1aDMQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgSwdaqx9cW9u2pdrdZ8lls9bkvh9OgKCUhNmHucOts4fL3WxIy1aDMQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\"><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\"># \u63d0\u53d6GSM ID\u4f5c\u4e3a\u6837\u54c1\u540d\uff0cpData\u51fd\u6570\u6765\u83b7\u53d6\u6837\u672c\u4fe1\u606f<\/span><\/code><code><span class=\"code-snippet_outer\">GSMID <- pData(eset)[,c(<span class=\"code-snippet__number\">1<\/span>,<span class=\"code-snippet__number\">2<\/span>,<span class=\"code-snippet__number\">8<\/span>,<span class=\"code-snippet__number\">10<\/span>,<span class=\"code-snippet__number\">12<\/span>)]<\/span><\/code><\/pre>\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=\"0.3194945848375451\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_5uSdKtaj2qCvYHMAjymNHE2NrkzAZw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgiaAl1U8Y9hgK78p2Ayg0Hp1Om5uSdKtaj2qCvYHMAjymNHE2NrkzAZw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" data-recalc-dims=\"1\"><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u6574\u7406\u82af\u7247\u6ce8\u91ca\u4fe1\u606f<\/span><\/code><code><span class=\"code-snippet_outer\">colnames(exprSet) <- GSMID$geo_accession<\/span><\/code><code><span class=\"code-snippet_outer\"># \u83b7\u5f97\u63a2\u91dd\u7ec4\u8ddfgene symbol\u7684\u5bf9\u5e94\u5173\u7cfb<\/span><\/code><code><span class=\"code-snippet_outer\">gpl <- getGEO(eset$platform_id[<span class=\"code-snippet__number\">1<\/span>])<\/span><\/code><code><span class=\"code-snippet_outer\">dim(Table(gpl)) #\u67e5\u770b\u4e00\u5171\u6709\u591a\u5c11\u884c\u63a2\u9488\u7ec4<\/span><\/code><code><span class=\"code-snippet_outer\"># \u63d0\u53d6\u81ea\u5df1\u60f3\u8981\u7684\u4fe1\u606f\uff0c\u6b64\u5904\u7b2c<span class=\"code-snippet__number\">1<\/span>\u3001<span class=\"code-snippet__number\">11<\/span>\u3001<span class=\"code-snippet__number\">12<\/span>\u5217\uff0c\u5206\u522b\u662f\u884c\u540dID\u548c\u5176\u5bf9\u5e94\u7684Gene Symbol\u548cENTREZ_GENE_ID<\/span><\/code><code><span class=\"code-snippet_outer\">annotation <- Table(gpl)[,c(<span class=\"code-snippet__number\">1<\/span>,<span class=\"code-snippet__number\">11<\/span>,<span class=\"code-snippet__number\">12<\/span>)]<\/span><\/code><\/pre>\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=\"0.18772563176895307\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-19_\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790\/6_LsY0CGcntacqz3am2D11wnZuoiczrw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgQ11P6y6Ww12HnSN8rwrYbdY9XLsY0CGcntacqz3am2D11wnZuoiczrw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\"><\/p>\n<\/section>\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=\"c\"><code><span class=\"code-snippet_outer\">#\u5c06factor \u6539\u4e3a character<\/span><\/code><code><span class=\"code-snippet_outer\">i <- sapply(annotation, is.factor) # Change factor to character<\/span><\/code><code><span class=\"code-snippet_outer\">annotation[i] <- lapply(annotation[i], as.character)<\/span><\/code><code><span class=\"code-snippet_outer\"># \u6709\u4e9b\u63a2\u9488\u7ec4\u5bf9\u5e94\u591a\u500b\u57fa\u56e0\uff0c\u4f7f\u7528\u201c<span class=\"code-snippet__comment\">\/\/\/\u201d\u5206\u5272\uff0c\u7576\u7136\u4f60\u53ef\u4ee5\u9009\u62e9\u4fdd\u7559\uff0c\u6211\u7684\u4e60\u60ef\u662f\u4fdd\u7559\u7b2c\u4e00\u4e2a<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">annotation[,<span class=\"code-snippet__number\">2<\/span>]<-data.frame(sapply(annotation[,<span class=\"code-snippet__number\">2<\/span>],function(x) unlist(strsplit(x,<span class=\"code-snippet__string\">'\/\/\/'<\/span>))[<span class=\"code-snippet__number\">1<\/span>]),stringsAsFactors = F)[,<span class=\"code-snippet__number\">1<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\">annotation[,<span class=\"code-snippet__number\">3<\/span>]<-data.frame(sapply(annotation[,<span class=\"code-snippet__number\">3<\/span>],function(x) unlist(strsplit(x,<span class=\"code-snippet__string\">'\/\/\/'<\/span>))[<span class=\"code-snippet__number\">1<\/span>]),stringsAsFactors = F)[,<span class=\"code-snippet__number\">1<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\"># \u628a\u6574\u7406\u597d\u7684\u63a2\u9488\u7ec4ID\u3001gene symbol\u3001ENTREZ ID\u5bf9\u5e94\u5173\u7cfb\u4fdd\u5b58\u5230\u6587\u4ef6\u91cc<\/span><\/code><code><span class=\"code-snippet_outer\">colnames(annotation) <- c(<span class=\"code-snippet__string\">\"probe_id\"<\/span>, <span class=\"code-snippet__string\">\"gsym\"<\/span>, <span class=\"code-snippet__string\">\"entrez_id\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">write.csv(annotation, <span class=\"code-snippet__string\">\"gplTOgene.csv\"<\/span>, row.names = F)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p><code><span style=\"font-size: 14px;\">#\u5c0f\u679c\u6765\u753b\u91cd\u70b9\u5566\uff01\u4e0d\u540c\u7684\u6d4b\u5e8f\u5e73\u53f0\u82af\u7247\u6ce8\u91ca\u4fe1\u606f\u53ef\u80fd\u6709\u5dee\u5f02\u5965\uff0c\u5728\u63d0\u53d6\u6ce8\u91ca\u4fe1\u606f\u7684\u65f6\u5019\u8981\u6839\u636e\u4e0d\u540c\u5e73\u53f0\u683c\u5f0f\u7075\u6d3b\u5904\u7406\uff0c\u672c\u5b9e\u4f8b\u6570\u636e\u6d4b\u5e8f\u5e73\u53f0\u4e3aGPL3912\uff0c\u53ef\u4ee5\u70b9\u51fb\u67e5\u770b\u6ce8\u91ca\u4fe1\u606f\u5185\u5bb9\u3002<\/span><\/code><code><span style=\"font-size: 14px;\">\u70b9\u51fbGPL3912\uff0c\u5c31\u53ef\u4ee5\u770b\u5230\u82af\u7247\u5b8c\u6574\u6ce8\u91ca\u4fe1\u606f\uff1a<\/span><\/code><\/p>\n<p><code><br \/><\/code><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.20397111913357402\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_y0dchh0EhIiaA1F0Geh38aPFJdAgqw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgxKp4OwL6WWrfIXKuib8YKXdhZNy0dchh0EhIiaA1F0Geh38aPFJdAgqw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" data-recalc-dims=\"1\"><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3562386980108499\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-19_\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790\/8_K84r3BHBVYk4icoRibpbmDInnPvF1Q.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2Xg0ia4QG0jMHOvIJsoy7gg25yN5XmK84r3BHBVYk4icoRibpbmDInnPvF1Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"553\"><\/p>\n<p><br \/><\/p>\n<p><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;letter-spacing: 0.578px;font-size: 16px;margin-bottom: 0px;white-space: normal;\"><span style=\"font-size: 14px;\"><strong style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;white-space: normal;\"><em><span style=\"font-size: 20px;\"> 4.\u628a\u8868\u8fbe\u77e9\u9635\u7684\u63a2\u9488ID\u6362\u6210Gene Symbol<\/span><\/em><\/strong><\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">annotation <- read.csv(<span class=\"code-snippet__string\">\"gplTOgene.csv\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">head(annotation)<\/span><\/code><\/pre>\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=\"0.18592057761732853\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_4B8ulY8zyKDavgRh4Ev9TK8UGIxbeQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgDgssANsNxxlrFt3Y4xjib1EpS4B8ulY8zyKDavgRh4Ev9TK8UGIxbeQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" data-recalc-dims=\"1\"><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u5c06\u63a2\u9488\u4fe1\u606f\u548c\u8868\u8fbe\u77e9\u9635\u5408\u5e76<\/span><\/code><code><span class=\"code-snippet_outer\">exprSet$probe_id <- rownames(exprSet)<\/span><\/code><code><span class=\"code-snippet_outer\">express <- merge(x = exprSet, y = annotation[,c(<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">2<\/span>)], by = <span class=\"code-snippet__string\">\"probe_id\"<\/span>, all.x = T)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3249097472924188\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-19_\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790\/10_toNL9DUnnoZN9hY9LlznwLppyiaYog.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2Xg1tTxQCiccdwVB2327u8xzTQpk0toNL9DUnnoZN9hY9LlznwLppyiaYog\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\"><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u53bb\u9664probe_id\u8fd9\u5217\u4fe1\u606f<\/span><\/code><code><span class=\"code-snippet_outer\">express$probe_id <- <span class=\"code-snippet__literal\">NULL<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"># \u6709\u4e9bgene\u5bf9\u5e94\u591a\u4e2a\u63a2\u9488\u7ec4\uff0c\u6b64\u5904\u4fdd\u7559\u5176\u4e2d\u8868\u8fbe\u91cf\u6700\u5927\u503c<\/span><\/code><code><span class=\"code-snippet_outer\">rowMeans <- apply(express, <span class=\"code-snippet__number\">1<\/span>, function(x) mean(as.numeric(x), na.rm = T))<\/span><\/code><code><span class=\"code-snippet_outer\">express <- express[order(rowMeans, decreasing =T),]<\/span><\/code><code><span class=\"code-snippet_outer\">express <- express[!duplicated(express[, dim(express)[<span class=\"code-snippet__number\">2<\/span>]]),] <span class=\"code-snippet__meta\">#express\u7684\u6700\u540e\u4e00\u5217\u4e3agene name<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">express <- na.omit(express)<\/span><\/code><code><span class=\"code-snippet_outer\">dim(express)<\/span><\/code><\/pre>\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=\"0.11552346570397112\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_XxvrMZmSU4NEzeiaSS4Afq8gdp0OEA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2Xg9RcWsehPrEfeIlWeFA21uqVTzXxvrMZmSU4NEzeiaSS4Afq8gdp0OEA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" data-recalc-dims=\"1\"><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u5c06\u6700\u540e\u4e00\u5217\u4f5c\u4e3a\u884c\u540d<\/span><\/code><code><span class=\"code-snippet_outer\">rownames(express) <- express[,dim(express)[<span class=\"code-snippet__number\">2<\/span>]]<\/span><\/code><code><span class=\"code-snippet_outer\">#\u5220\u9664\u6700\u540e\u4e00\u5217<\/span><\/code><code><span class=\"code-snippet_outer\">express <- express[,-(dim(express)[<span class=\"code-snippet__number\">2<\/span>])]<\/span><\/code><code><span class=\"code-snippet_outer\"># \u8868\u8fbe\u77e9\u9635\uff08express\uff09\u5df2\u6784\u5efa\u597d\uff0c\u4fdd\u5b58\u5230\u6587\u4ef6<\/span><\/code><code><span class=\"code-snippet_outer\">write.csv(express, <span class=\"code-snippet__string\">\"easy_input_expr.csv\"<\/span>, quote = F)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p powered-by=\"xiumi.us\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p powered-by=\"xiumi.us\" style=\"text-align: center;letter-spacing: 0.578px;font-size: 16px;margin-bottom: 0px;white-space: normal;\"><span style=\"font-size: 14px;\"><strong style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;white-space: normal;\"><em><span style=\"font-size: 20px;\">5.\u6309\u7167\u5b9e\u9a8c\u8bbe\u8ba1\u6574\u7406\u5206\u7ec4\u4fe1\u606f<\/span><\/em><\/strong><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">pdata <- pData(eset)<\/span><\/code><code><span class=\"code-snippet_outer\">i <- sapply(pdata, is.factor)<\/span><\/code><code><span class=\"code-snippet_outer\">pdata[i] <- lapply(pdata[i], as.character)<\/span><\/code><code><span class=\"code-snippet_outer\"># \u6309\u7167\u5b9e\u9a8c\u8bbe\u8ba1\uff0c\u6784\u5efa\u5206\u7ec4\u77e9\u9635<\/span><\/code><code><span class=\"code-snippet_outer\">group_list <- subset(pdata, select = title) # Sample\u7684\u5206\u7ec4\u4fe1\u606f<\/span><\/code><code><span class=\"code-snippet_outer\">group_list$condition = rep(c(<span class=\"code-snippet__string\">\"a\"<\/span>,<span class=\"code-snippet__string\">\"b\"<\/span>), each = <span class=\"code-snippet__number\">3<\/span>)<\/span><\/code><\/pre>\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=\"0.2786885245901639\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/12_HwSwrSCz9IoicAAiajTmibINwu5m7A.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgNKd5lBAsUxBPbycibvK8mjFqic8erHwSwrSCz9IoicAAiajTmibINwu5m7A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"488\" data-recalc-dims=\"1\"><\/p>\n<p><br \/><\/p>\n<p><span style=\"font-size: 14px;\">#\u5206\u7ec4\u77e9\u9635\uff08design\uff09\u5df2\u6784\u5efa\u597d<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">write.table(group_list, <span class=\"code-snippet__string\">\"easy_input_pheno.txt\"<\/span>, quote = F, sep = <span class=\"code-snippet__string\">\"t\"<\/span>, row.names = F)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p><br \/><\/p>\n<p style=\"text-align: center;letter-spacing: 0.578px;font-size: 16px;margin-bottom: 0px;white-space: normal;\"><span style=\"font-size: 14px;\"><strong style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;white-space: normal;\"><em><span style=\"font-size: 20px;\">6.\u5229\u7528limma \u5305\u8fdb\u884c\u5dee\u5f02\u5206\u6790<\/span><\/em><\/strong><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u4e0d\u505a\u5747\u4e00\u5316\u5904\u7406<\/span><\/code><code><span class=\"code-snippet_outer\">express.norm <- express<\/span><\/code><code><span class=\"code-snippet_outer\">#\u751f\u6210\u6a21\u578b\u8bbe\u8ba1\u77e9\u9635<\/span><\/code><code><span class=\"code-snippet_outer\">design <- model.matrix(~ <span class=\"code-snippet__number\">0<\/span> + factor(group_list$condition))<\/span><\/code><code><span class=\"code-snippet_outer\">#\u66ff\u6362\u5217\u540d<\/span><\/code><code><span class=\"code-snippet_outer\">colnames(design) <- levels(factor(group_list$condition))<\/span><\/code><code><span class=\"code-snippet_outer\">#\u66ff\u6362\u884c\u540d<\/span><\/code><code><span class=\"code-snippet_outer\">rownames(design) <- colnames(express.norm)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3862815884476534\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-19_\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790\/13_MUx9Ek2VO9RAJCgqylAPEh7mdjZzFA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgRgMnpxyXSRYNGIEKEcWb3SiaxMUx9Ek2VO9RAJCgqylAPEh7mdjZzFA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\"><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u6784\u5efa\u6bd4\u8f83\u77e9\u9635<\/span><\/code><code><span class=\"code-snippet_outer\">contrast.matrix <- makeContrasts(b-a, levels = design)<\/span><\/code><\/pre>\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=\"0.10649819494584838\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/14_776DUPvnLV6CicXMS8XZ0IpdvrY3mg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgdlQma2zNTGib8AghxtHmtKLTAc776DUPvnLV6CicXMS8XZ0IpdvrY3mg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" data-recalc-dims=\"1\"><\/p>\n<\/section>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u7ebf\u6027\u6a21\u578b\u62df\u5408<\/span><\/code><code><span class=\"code-snippet_outer\">fit <- lmFit(express.norm,design)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u8ba1\u7b97estimated coefficient \u548c\u6807\u51c6\u8bef\u5dee<\/span><\/code><code><span class=\"code-snippet_outer\">fit2 <- contrasts.fit(fit,contrast.matrix)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u5dee\u5f02\u5206\u6790<\/span><\/code><code><span class=\"code-snippet_outer\">fit2 <- eBayes(fit2)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u63d0\u53d6\u6240\u6709\u5dee\u5f02\u57fa\u56e0\u8868\u683c\uff0c\u884c\u540d\u4e3aGene symbol,\u5217\u540d\u4e3b\u8981\u5173\u6ce8logFC,P.Value\u548cadj.P.Val\uff0c\u901a\u8fc7pvalue\u503c\u6392\u5e8f\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">x <- topTable(fit2, coef = <span class=\"code-snippet__number\">1<\/span>, n = Inf, adjust.method = <span class=\"code-snippet__string\">\"fdr\"<\/span>, sort.by = <span class=\"code-snippet__string\">\"P\"<\/span>)<\/span><\/code><\/pre>\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=\"0.1967509025270758\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/15_E7nBIlj2lym54Usv7JHb3r8rzETibw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgMnzplSYveJibVJib92xT0OoiaPSYE7nBIlj2lym54Usv7JHb3r8rzETibw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" data-recalc-dims=\"1\"><span style=\"font-size: 14px;letter-spacing: 0.578px;text-align: justify;\"> <\/span><\/p>\n<p><span style=\"font-size: 14px;\">#\u628a\u5168\u90e8\u57fa\u56e0\u7684limma\u5206\u6790\u7ed3\u679c\u4fdd\u5b58\u5230\u6587\u4ef6<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">write.csv(x, <span class=\"code-snippet__string\">\"limma.csv\"<\/span>, quote = F)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;\"><span style=\"font-size: 14px;\"><strong style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;white-space: normal;\"><em><span style=\"font-size: 20px;\">7.\u7ed3\u679c\u6587\u4ef6<\/span><\/em><\/strong><\/span><\/p>\n<section powered-by=\"xiumi.us\" style=\"margin-bottom: 0px;font-size: 16px;letter-spacing: 0.578px;white-space: normal;\">\n<p style=\"margin-bottom: 0px;font-size: 16px;letter-spacing: 0.578px;white-space: normal;\"><strong><span style=\"font-size: 14px;\">1. gplTOgene.csv<\/span><\/strong><\/p>\n<p><span style=\"font-size: 14px;\">\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u63a2\u9488id\u5bf9\u5e94\u7684Gene symbol\u548centrez_id\uff0c\u7b2c\u4e00\u5217\u4e3a\u63a2\u9488ID\uff0c\u7b2c\u4e8c\u5217\u4e3aGene symbol,\u7b2c\u4e09\u5217\u4e3aentrez_id\u3002<\/span><\/p>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.5342960288808665\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-19_\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790\/16_n0ZYA6SzK0TPEjeM3hib98jHD83CMw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgFibsZoxxDNmh2Utm3icL9TO3de5n0ZYA6SzK0TPEjeM3hib98jHD83CMw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\"><\/p>\n<p><span style=\"font-size: 14px;\"><\/span><\/p>\n<p><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"letter-spacing: 0.578px;font-size: 16px;margin-bottom: 0px;white-space: normal;\"><strong><span style=\"font-size: 14px;\">2. easy_input_expr.csv<\/span><\/strong><\/p>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;\">\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u5904\u7406\u597d\u7684\u8868\u8fbe\u77e9\u9635\u6587\u4ef6\uff0c\u884c\u540d\u4e3aGene symbol,\u5217\u540d\u4e3a\u5bf9\u5e94\u7684\u6837\u672c\u540d\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.4548736462093863\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/17_JOxnV9dPEG3ibJbCv6EL8gpRdldwqg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgofLuWH5cpeAYKtj21LmKa6aKiaJOxnV9dPEG3ibJbCv6EL8gpRdldwqg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" data-recalc-dims=\"1\"><\/p>\n<p><span style=\"font-size: 14px;\"><\/span><\/p>\n<p><br \/><\/p>\n<p><span style=\"font-size: 14px;\"> <\/span><strong><span style=\"font-size: 14px;\">3. easy_input_pheno.txt<\/span><\/strong><\/p>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;\">\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u63d0\u53d6\u7684\u6837\u672c\u5206\u7ec4\u6587\u4ef6\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.17148014440433212\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-19_\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790\/18_7AwEyuKhURSmcRMhVrIsv6T23CdgSg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgPsqe0FO5pp2liaVlGZRk0AjFn7AwEyuKhURSmcRMhVrIsv6T23CdgSg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\"><\/p>\n<p><span style=\"font-size: 14px;\"><\/span><\/p>\n<p style=\"letter-spacing: 0.578px;font-size: 16px;margin-bottom: 0px;white-space: normal;\"><span style=\"font-size: 14px;\"><strong> 4. easy_input_limma.csv<\/strong><\/span><\/p>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;\">\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u901a\u8fc7limma\u5305\u8fdb\u884c\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u6587\u4ef6\uff0c\u884c\u540d\u4e3aGene symbol,\u7b2c\u4e00\u5217\u4e3alog2FC\uff0c\u7b2c\u56db\u5217\u4e3aPvalue\u503c\uff0c\u7b2c\u4e94\u5217\u4e3a\u77eb\u6b63\u540e\u7684Pvalue\u503c\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.4602888086642599\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/19_QEK18GevNlleGTVKtVeib09oLPpu8Q.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgfottWrBEHkKSwaRhV6JKw71sMQEK18GevNlleGTVKtVeib09oLPpu8Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" data-recalc-dims=\"1\"><\/p>\n<p><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u4eca\u5929\u5c0f\u679c\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\u5566\uff01\u5982\u679c\u5c0f\u4f19\u4f34\u6709\u5176\u4ed6\u6570\u636e\u5206\u6790\u9700\u6c42\uff0c\u53ef\u4ee5\u5c1d\u8bd5\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\uff1ahttp:\/\/www.biocloudservice.com\/home.html,\u5305\u62ec\u4e86GEO\u6570\u636e\u4e0b\u8f7d(http:\/\/www.biocloudservice.com\/371\/371.php),limma+gsva(http:\/\/www.biocloudservice.com\/371\/371.php)\u7b49\u5c0f\u5de5\u5177\uff0c\u6b22\u8fce\u5927\u5bb6\u548c\u5c0f\u679c\u4e00\u8d77\u8ba8\u8bba\u5b66\u4e60\u54c8\uff01\uff01\uff01\uff01<\/span><\/p>\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=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;font-size: 16px;\">\n<section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section data-tools=\"135\u7f16\u8f91\u5668\" data-id=\"105054\" style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;font-size: 16px;\">\n<section style=\"margin: 10px auto;text-align: center;\">\n<section style=\"padding-top: 30px;padding-bottom: 30px;background-color: rgb(242, 246, 255);border-radius: 7px;\">\n<section style=\"display: flex;justify-content: space-evenly;align-items: center;\">\n<section data-width=\"26%\" style=\"width: 150.266px;\">\n<section style=\"padding: 7px;border-radius: 15px;box-shadow: rgba(169, 187, 223, 0.45) 4px 4px 8px, rgb(255, 255, 255) -2.5px -2.5px 5px;\">\n<section data-width=\"100%\" style=\"width: 136.266px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-cropselx1=\"0\" data-cropselx2=\"136\" data-cropsely1=\"0\" data-cropsely2=\"137\" data-ratio=\"1\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-19_\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790\/20_jEYQoRbKh3HUg3IGgzymibpTnmaM6Q.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwIX3hF1ZZeqvXLknM5Oq7CDG9YFpmvU1ge12vc3NvibhViceQjEYQoRbKh3HUg3IGgzymibpTnmaM6Q\/640?wx_fmt=jpeg'\" data-type=\"png\" data-w=\"430\" data-width=\"100%\" style=\"height: 137px;vertical-align: inherit;width: 137px;display: block;border-radius: 7px;\" title=\"\u5c0f\u4e91-\u5fae\u4fe1\u4e8c\u7ef4\u7801.png\" \/><\/section>\n<\/section>\n<\/section>\n<section data-width=\"62%\" style=\"width: 358.359px;\">\n<section style=\"display: inline-block;\">\n<section style=\"padding: 7px 15px;border-radius: 20px;box-shadow: rgba(169, 187, 223, 0.45) 6px 6px 8px inset, rgb(255, 255, 255) -2.5px -2.5px 5px inset;\">\n<section data-brushtype=\"text\" style=\"font-size: 14px;letter-spacing: 1.5px;color: rgb(111, 133, 172);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><span style=\"letter-spacing: 1.5px;\">\u626b\u7801\u52a0\u5c0f\u679c<\/span><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><span style=\"letter-spacing: 1.5px;\">\u9886\u53d6\u751f\u4fe1\u5927\u793c\u5305<\/span><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;caret-color: rgba(0, 0, 0, 0);font-size: 16px;\">\n<section>\n<section style=\"margin-top: 0.5em;\">\n<section style=\"padding: 0.5em;border-width: 1px;border-style: solid;box-shadow: rgb(226, 226, 226) 0px 16px 1px -13px;border-color: rgb(0, 150, 136);\">\n<section style=\"text-align: left;\">\n<section style=\"color: rgb(255, 129, 36);text-align: justify;\">\n<section style=\"margin-bottom: 8px;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u70b9\u51fb<strong><span style=\"color: rgb(0, 150, 136);\">\u201c\u9605\u8bfb\u539f\u6587\u201d<\/span><\/strong>\u7acb\u523b\u62e5\u6709<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: 8px;font-size: 32px;color: rgb(0, 150, 136);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u2193\u2193\u2193 <\/span><span style=\"letter-spacing: 0.5px;text-indent: 0em;\"><\/span><\/p>\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<p style=\"display: none;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<p><\/content><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790 \u539f\u521b \u5c0f\u679c &nbsp 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0;align-items:center}.flex_bd{padding-left:14px;}.account_nickname{display:inline-block;vertical-align:middle;line-height:1.2;color:#576b95;font-size:14px}.account_desc{overflow:hidden;text-overflow:ellipsis;display:-webkit-box;-webkit-box-orient:vertical;-webkit-line-clamp:1;color:rgba(0,0,0,0.3);font-size:14px;line-height:1.2;padding-top:.4em}.msg_source_url{text-align:left;word-break:break-all;margin-top:20px;}.msg_source_url a{padding-right:10px;}.msg_source_url .url_text{color:#a8a8a8;}.video-desc{font-size:14px;margin-top:15px;color:#6c6c6c;}.msg_source_url{text-align:left;}.original_primary_card_tips{color:rgba(0,0,0,0.3);line-height:1.4;font-size:15px;}.weui-flex__item{margin-bottom:20px;padding:20px 16px;margin-top:16px;line-height:1.4;align-items:center;background-color:#f7f7f7;border-radius:8px;position:relative;}.original_primary_desc{color:rgba(0,0,0,0.5);font-size:14px;padding-top:4px;width:auto;overflow:hidden;text-overflow:ellipsis;}.msgBodyReplyList{border-top:1px solid #e1e1e1;margin-top:10px;}.msgBodyReplyListTop{border-top:0;}.reply_like_num{float:right;font-size:14px;color:#c7c7c7;}.msgData{margin-top:20px;color:#626262;}.msgData span{font-size:14px;padding-right:15px;}.msgData .likes{float:right;padding-right:0;}.js_text_content p{font-size:18px;}.rich_media_meta_link{font-size:15px;}blockquote {padding-left: 10px;border-left: 3px solid #dbdbdb;color: rgba(0,0,0,0.5);font-size: 15px;padding-top: 4px;margin: 1em 0;}.video_iframe{width:500px;height:400px;}.blockquote_info{color:#b5b5b5;margin-top:10px;}#copyright_logo{color:#bdbdbd;}.rich_media_meta_list{margin-bottom:10px;}.reprint{background:#efefef;border-radius:5px;padding:8px;color:#1f1f1f;}.reprint a{word-break:break-all;}.topic{color:#8e8e8e;background:#f7f7f7;border-radius:5px;padding:10px 8px;}.topic a{padding-right:5px;}.topic p{margin-bottom:5px;}\n<\/style>\n<link href=\"https:\/\/www.juyifx.cn\/config\/css\/wxArticle.css\" rel=\"stylesheet\"\/>\n<\/head><script>\nvar 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class=\"rich_media_meta rich_media_meta_text\">\u5c0f\u679c <\/span><span class=\"rich_media_meta rich_media_meta_nickname\" id=\"profileBt\"><a href=\"javascript:void(0);\" class=\"wx_tap_link js_wx_tap_highlight weui-wa-hotarea\" id=\"js_name\">\u751f\u4fe1\u679c <\/a><\/span><em id=\"publish_time\" class=\"rich_media_meta rich_media_meta_text\">2023-06-19 19:00:34<\/em><\/div>\n<p><content><\/p>\n<section style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;font-size: 16px;\">\n<section>\n<section>\n<section>\n<section>\n<section>\n<section data-width=\"100%\" style=\"width: 578px;flex: 0 0 100%;opacity: 1;\">\n<section style=\"line-height: 1.8;\">\n<section>\n<section>\n<section style=\"margin-top: 10px;margin-bottom: 20px;display: flex;flex-flow: row nowrap;text-align: center;justify-content: center;\">\n<section style=\"display: inline-block;width: 578px;vertical-align: top;border-style: solid;border-width: 1px;border-color: rgb(67, 67, 67);flex: 0 0 auto;align-self: flex-start;height: auto;box-shadow: rgb(255, 219, 118) 6px 6px 0px;background-color: rgb(255, 255, 255);\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;\">\n<section style=\"display: inline-block;width: 403.391px;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;\">\n<section style=\"margin-top: 10px;\">\n<section style=\"text-align: center;\">\n<section style=\"font-size: 16px;\">\n<section style=\"\" powered-by=\"xiumi.us\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;\">\n<section style=\"display: inline-block;vertical-align: top;width: 70.0348%;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 70.0348% !important;\">\n<section style=\"margin-top: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 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% !important;\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;line-height: 0;\">\n<section>\n<section style=\"display: inline-block;vertical-align: middle;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 0;\">\n<section style=\"width: 111px;\" powered-by=\"xiumi.us\">\n<section style=\"line-height: 1.75em;text-indent: 0em;\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;height: auto;width: 111px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_GBhsibRAgNiaQsH4ichdP9ibEhHMFA-103.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyL6u7wJswOp8vtpzGp6vYngnlT6jiavu08Bvp2iblzGf3IkoBD9NGBhsibRAgNiaQsH4ichdP9ibEhHMFA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"400\" style=\"vertical-align: middle;width: 100%;\" 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<p style=\"text-indent: 0em;line-height: 1.75em;\"><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section data-role=\"list\">\n<section>\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 8px;text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;\">\n<section style=\"padding-left: 8px;display: inline-block;width: 578px;vertical-align: top;border-left: 3px solid rgb(219, 219, 219);border-bottom-left-radius: 0px;align-self: flex-start;flex: 0 0 auto;\">\n<section powered-by=\"xiumi.us\" style=\"color: rgba(0, 0, 0, 0.5);text-align: justify;\">\n<p><span style=\"letter-spacing: 0.578px;\"><span style=\"font-size: 14px;letter-spacing: 0.578px;\"><span style=\"letter-spacing: 0.578px;\"><span style=\"font-size: 14px;letter-spacing: 0.578px;\">\u901a\u8fc7\u8be5\u63a8\u6587\uff0c\u4f60\u5c06\u5b8c\u5168\u638c\u63e1GEO\u516c\u5171\u6570\u636e\u4e0b\u8f7d\u548c\u5dee\u5f02\u5206\u6790\uff0c\u975e\u5e38\u975e\u5e38\u9002\u5408\u5c0f\u767d\uff0c\u5982\u679c\u4f60\u6709\u6570\u636e\u6316\u6398\u7684\u60f3\u6cd5\uff0c\u63a5\u4e0b\u6765\u9a6c\u4e0a\u8ddf\u7740\u5c0f\u679c\u5f00\u59cb\u4eca\u5929\u7684\u5b66\u4e60\u4e4b\u65c5\uff0c\u76f8\u4fe1\u4f60\u4f1a\u6536\u83b7\u6ee1\u6ee1\u3002<\/span><\/span><\/span><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section style=\"font-size: 16px;\">\n<section powered-by=\"xiumi.us\" style=\"letter-spacing: 0.578px;\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;\"><span style=\"font-size: 14px;\"><strong style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;white-space: normal;\"><em><span style=\"font-size: 20px;\">1. \u5982\u4f55\u83b7\u5f97\u76f8\u5173\u75be\u75c5\u7684GEO\u6570\u636e\u5e93ID<\/span><\/em><\/strong><\/span><\/p>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;\">\u5728\u8fdb\u884c\u5b9e\u64cd\u4e4b\u524d\uff0c\u6700\u91cd\u8981\u7684\u662f\u8981\u83b7\u5f97\u76f8\u5173\u75be\u75c5\u7684GEO\u6570\u636e\u5e93ID\uff0c\u5982\u4f55\u83b7\u5f97\u5462\uff1f\u4e0d\u614c\uff01\u5c0f\u679c\u4e3a\u5927\u5bb6\u4ecb\u7ecd\u4e24\u79cd\u5e38\u7528\u7684\u65b9\u6cd5\u3002\u7b2c\u4e00\u79cd\u65b9\u6cd5\u662f\u901a\u8fc7NCBI GEO DataSets \u6570\u636e\u5e93\u4e0b\u8f7d\uff0c\u53ef\u4ee5\u76f4\u63a5\u8f93\u5165\u60f3\u67e5\u8be2\u7684\u75be\u75c5\u540d\u79f0\u5c31\u53ef\u4ee5\u8fdb\u884c\u641c\u7d22\u83b7\u5f97\u76f8\u5e94\u7684\u6570\u636e\uff0c\u7f51\u5740\u4e3a\uff1ahttps:\/\/www.ncbi.nlm.nih.gov\/gds\/?term=GSE70494<\/span><span style=\"text-align: center;letter-spacing: 0.578px;\"><\/span><\/p>\n<p><span style=\"font-size: 14px;\"><\/span><span style=\"text-align: center;letter-spacing: 0.578px;\"><\/span><\/p>\n<p><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.34115523465703973\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-19_\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790\/2_OrxV1uoibMnIZZvVPibrLGkHraZLqQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgYQVVs6ZbiaDDfvynk5TeGeuXibIbOrxV1uoibMnIZZvVPibrLGkHraZLqQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\"><\/p>\n<p><span style=\"font-size: 14px;\"><\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u7b2c\u4e8c\u79cd\u65b9\u6cd5\u662f\u901a\u8fc7\u4ee5\u53d1\u8868\u7684\u6587\u732e\u6765\u67e5\u8be2\u76f8\u5173\u75be\u75c5\u7684GEO ID\uff0c\u5c0f\u679c\u662f\u901a\u8fc7PubMed\u6765\u67e5\u8be2\uff0c\u53ea\u9700\u8981\u8f93\u5165\u76f8\u5173\u75be\u75c5\u5173\u952e\u5b57\u548cGEO\u5c31\u53ef\u4ee5\u641c\u7d22\u5230\u76f8\u5173\u6587\u7ae0\u548cGEO ID\uff0c\u8be5\u7f51\u5740\u4e3a\uff1ahttps:\/\/pubmed.ncbi.nlm.nih.gov\/?term=gene+family<\/span><\/p>\n<p><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.29061371841155237\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_XHNopzS3fxdE77iccYfEYicAS9Ne7g.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgCxWWQsZJuxHmhiaSsM69qx9PCxiaXHNopzS3fxdE77iccYfEYicAS9Ne7g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" data-recalc-dims=\"1\"><\/p>\n<p><span style=\"font-size: 14px;\"><\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u4e00\u822c\u901a\u8fc7\u8fd9\u4e24\u79cd\u65b9\u6cd5\u5c31\u53ef\u4ee5\u83b7\u53d6\u81ea\u5df1\u60f3\u8981\u7684GEO ID\uff0c\u901a\u8fc7\u5c0f\u679c\u7684\u65b9\u6cd5\u83b7\u5f97ID\u540e\uff0c\u5c31\u53ef\u4ee5\u8ddf\u7740\u5c0f\u679c\u5f00\u59cb\u4eca\u5929\u7684\u5b9e\u64cd\u5206\u6790\u5566\uff0c\u5176\u5b9e\u5c31\u662f\u8fd9\u4e48\u7b80\u5355\uff01\uff01\uff01\u54c8\u54c8\u54c8\u54c8\u54c8\u3002\u3002\u3002\u3002\u3002\u3002\u3002\u3002<\/span><\/p>\n<p><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;letter-spacing: 0.578px;font-size: 16px;margin-bottom: 0px;white-space: normal;\"><span style=\"font-size: 14px;\"><strong style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;white-space: normal;\"><em><span style=\"font-size: 20px;\">2. \u5bfc\u5165\u9700\u8981\u7684R\u5305<\/span><\/em><\/strong><\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">library(GEOquery)<\/span><\/code><code><span class=\"code-snippet_outer\">library(limma)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<p powered-by=\"xiumi.us\" style=\"text-align: center;letter-spacing: 0.578px;font-size: 16px;margin-bottom: 0px;white-space: normal;\"><span style=\"font-size: 14px;\"><strong style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;white-space: normal;\"><em><span style=\"font-size: 20px;\">3. \u4eceGEO\u4e0b\u8f7d\u8868\u8fbe\u77e9\u9635\u548c\u82af\u7247\u6ce8\u91ca\u6ce8\u91ca\u6587\u4ef6<\/span><\/em><\/strong><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">GSEdata <- getGEO(<span class=\"code-snippet__string\">\"GSE17215\"<\/span>, GSEMatrix=T, AnnotGPL=FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">eset <- GSEdata[[<span class=\"code-snippet__number\">1<\/span>]]<\/span><\/code><code><span class=\"code-snippet_outer\">#\u63d0\u53d6\u8868\u8fbe\u77e9\u9635,\u901a\u8fc7exprs\u51fd\u6570\u63d0\u53d6\uff0c\u884c\u540d\u4e3a\u63a2\u9488ID\uff0c\u5217\u540d\u4e3a\u6837\u672c\u540d<\/span><\/code><code><span class=\"code-snippet_outer\">exprSet <- as.data.frame(exprs(eset))<\/span><\/code><\/pre>\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=\"0.18592057761732853\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-19_\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790\/4_vh9OgKCUhNmHucOts4fL3WxIy1aDMQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgSwdaqx9cW9u2pdrdZ8lls9bkvh9OgKCUhNmHucOts4fL3WxIy1aDMQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\"><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\"># \u63d0\u53d6GSM ID\u4f5c\u4e3a\u6837\u54c1\u540d\uff0cpData\u51fd\u6570\u6765\u83b7\u53d6\u6837\u672c\u4fe1\u606f<\/span><\/code><code><span class=\"code-snippet_outer\">GSMID <- pData(eset)[,c(<span class=\"code-snippet__number\">1<\/span>,<span class=\"code-snippet__number\">2<\/span>,<span class=\"code-snippet__number\">8<\/span>,<span class=\"code-snippet__number\">10<\/span>,<span class=\"code-snippet__number\">12<\/span>)]<\/span><\/code><\/pre>\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=\"0.3194945848375451\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_5uSdKtaj2qCvYHMAjymNHE2NrkzAZw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgiaAl1U8Y9hgK78p2Ayg0Hp1Om5uSdKtaj2qCvYHMAjymNHE2NrkzAZw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" data-recalc-dims=\"1\"><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u6574\u7406\u82af\u7247\u6ce8\u91ca\u4fe1\u606f<\/span><\/code><code><span class=\"code-snippet_outer\">colnames(exprSet) <- GSMID$geo_accession<\/span><\/code><code><span class=\"code-snippet_outer\"># \u83b7\u5f97\u63a2\u91dd\u7ec4\u8ddfgene symbol\u7684\u5bf9\u5e94\u5173\u7cfb<\/span><\/code><code><span class=\"code-snippet_outer\">gpl <- getGEO(eset$platform_id[<span class=\"code-snippet__number\">1<\/span>])<\/span><\/code><code><span class=\"code-snippet_outer\">dim(Table(gpl)) #\u67e5\u770b\u4e00\u5171\u6709\u591a\u5c11\u884c\u63a2\u9488\u7ec4<\/span><\/code><code><span class=\"code-snippet_outer\"># \u63d0\u53d6\u81ea\u5df1\u60f3\u8981\u7684\u4fe1\u606f\uff0c\u6b64\u5904\u7b2c<span class=\"code-snippet__number\">1<\/span>\u3001<span class=\"code-snippet__number\">11<\/span>\u3001<span class=\"code-snippet__number\">12<\/span>\u5217\uff0c\u5206\u522b\u662f\u884c\u540dID\u548c\u5176\u5bf9\u5e94\u7684Gene Symbol\u548cENTREZ_GENE_ID<\/span><\/code><code><span class=\"code-snippet_outer\">annotation <- Table(gpl)[,c(<span class=\"code-snippet__number\">1<\/span>,<span class=\"code-snippet__number\">11<\/span>,<span class=\"code-snippet__number\">12<\/span>)]<\/span><\/code><\/pre>\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=\"0.18772563176895307\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-19_\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790\/6_LsY0CGcntacqz3am2D11wnZuoiczrw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgQ11P6y6Ww12HnSN8rwrYbdY9XLsY0CGcntacqz3am2D11wnZuoiczrw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\"><\/p>\n<\/section>\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=\"c\"><code><span class=\"code-snippet_outer\">#\u5c06factor \u6539\u4e3a character<\/span><\/code><code><span class=\"code-snippet_outer\">i <- sapply(annotation, is.factor) # Change factor to character<\/span><\/code><code><span class=\"code-snippet_outer\">annotation[i] <- lapply(annotation[i], as.character)<\/span><\/code><code><span class=\"code-snippet_outer\"># \u6709\u4e9b\u63a2\u9488\u7ec4\u5bf9\u5e94\u591a\u500b\u57fa\u56e0\uff0c\u4f7f\u7528\u201c<span class=\"code-snippet__comment\">\/\/\/\u201d\u5206\u5272\uff0c\u7576\u7136\u4f60\u53ef\u4ee5\u9009\u62e9\u4fdd\u7559\uff0c\u6211\u7684\u4e60\u60ef\u662f\u4fdd\u7559\u7b2c\u4e00\u4e2a<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">annotation[,<span class=\"code-snippet__number\">2<\/span>]<-data.frame(sapply(annotation[,<span class=\"code-snippet__number\">2<\/span>],function(x) unlist(strsplit(x,<span class=\"code-snippet__string\">'\/\/\/'<\/span>))[<span class=\"code-snippet__number\">1<\/span>]),stringsAsFactors = F)[,<span class=\"code-snippet__number\">1<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\">annotation[,<span class=\"code-snippet__number\">3<\/span>]<-data.frame(sapply(annotation[,<span class=\"code-snippet__number\">3<\/span>],function(x) unlist(strsplit(x,<span class=\"code-snippet__string\">'\/\/\/'<\/span>))[<span class=\"code-snippet__number\">1<\/span>]),stringsAsFactors = F)[,<span class=\"code-snippet__number\">1<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\"># \u628a\u6574\u7406\u597d\u7684\u63a2\u9488\u7ec4ID\u3001gene symbol\u3001ENTREZ ID\u5bf9\u5e94\u5173\u7cfb\u4fdd\u5b58\u5230\u6587\u4ef6\u91cc<\/span><\/code><code><span class=\"code-snippet_outer\">colnames(annotation) <- c(<span class=\"code-snippet__string\">\"probe_id\"<\/span>, <span class=\"code-snippet__string\">\"gsym\"<\/span>, <span class=\"code-snippet__string\">\"entrez_id\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">write.csv(annotation, <span class=\"code-snippet__string\">\"gplTOgene.csv\"<\/span>, row.names = F)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p><code><span style=\"font-size: 14px;\">#\u5c0f\u679c\u6765\u753b\u91cd\u70b9\u5566\uff01\u4e0d\u540c\u7684\u6d4b\u5e8f\u5e73\u53f0\u82af\u7247\u6ce8\u91ca\u4fe1\u606f\u53ef\u80fd\u6709\u5dee\u5f02\u5965\uff0c\u5728\u63d0\u53d6\u6ce8\u91ca\u4fe1\u606f\u7684\u65f6\u5019\u8981\u6839\u636e\u4e0d\u540c\u5e73\u53f0\u683c\u5f0f\u7075\u6d3b\u5904\u7406\uff0c\u672c\u5b9e\u4f8b\u6570\u636e\u6d4b\u5e8f\u5e73\u53f0\u4e3aGPL3912\uff0c\u53ef\u4ee5\u70b9\u51fb\u67e5\u770b\u6ce8\u91ca\u4fe1\u606f\u5185\u5bb9\u3002<\/span><\/code><code><span style=\"font-size: 14px;\">\u70b9\u51fbGPL3912\uff0c\u5c31\u53ef\u4ee5\u770b\u5230\u82af\u7247\u5b8c\u6574\u6ce8\u91ca\u4fe1\u606f\uff1a<\/span><\/code><\/p>\n<p><code><br \/><\/code><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.20397111913357402\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_y0dchh0EhIiaA1F0Geh38aPFJdAgqw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgxKp4OwL6WWrfIXKuib8YKXdhZNy0dchh0EhIiaA1F0Geh38aPFJdAgqw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" data-recalc-dims=\"1\"><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3562386980108499\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-19_\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790\/8_K84r3BHBVYk4icoRibpbmDInnPvF1Q.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2Xg0ia4QG0jMHOvIJsoy7gg25yN5XmK84r3BHBVYk4icoRibpbmDInnPvF1Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"553\"><\/p>\n<p><br \/><\/p>\n<p><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;letter-spacing: 0.578px;font-size: 16px;margin-bottom: 0px;white-space: normal;\"><span style=\"font-size: 14px;\"><strong style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;white-space: normal;\"><em><span style=\"font-size: 20px;\"> 4.\u628a\u8868\u8fbe\u77e9\u9635\u7684\u63a2\u9488ID\u6362\u6210Gene Symbol<\/span><\/em><\/strong><\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">annotation <- read.csv(<span class=\"code-snippet__string\">\"gplTOgene.csv\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">head(annotation)<\/span><\/code><\/pre>\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=\"0.18592057761732853\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_4B8ulY8zyKDavgRh4Ev9TK8UGIxbeQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgDgssANsNxxlrFt3Y4xjib1EpS4B8ulY8zyKDavgRh4Ev9TK8UGIxbeQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" data-recalc-dims=\"1\"><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u5c06\u63a2\u9488\u4fe1\u606f\u548c\u8868\u8fbe\u77e9\u9635\u5408\u5e76<\/span><\/code><code><span class=\"code-snippet_outer\">exprSet$probe_id <- rownames(exprSet)<\/span><\/code><code><span class=\"code-snippet_outer\">express <- merge(x = exprSet, y = annotation[,c(<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">2<\/span>)], by = <span class=\"code-snippet__string\">\"probe_id\"<\/span>, all.x = T)<\/span><\/code><\/pre>\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=\"0.3249097472924188\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-19_\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790\/10_toNL9DUnnoZN9hY9LlznwLppyiaYog.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2Xg1tTxQCiccdwVB2327u8xzTQpk0toNL9DUnnoZN9hY9LlznwLppyiaYog\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\"><\/p>\n<\/section>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u53bb\u9664probe_id\u8fd9\u5217\u4fe1\u606f<\/span><\/code><code><span class=\"code-snippet_outer\">express$probe_id <- <span class=\"code-snippet__literal\">NULL<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"># \u6709\u4e9bgene\u5bf9\u5e94\u591a\u4e2a\u63a2\u9488\u7ec4\uff0c\u6b64\u5904\u4fdd\u7559\u5176\u4e2d\u8868\u8fbe\u91cf\u6700\u5927\u503c<\/span><\/code><code><span class=\"code-snippet_outer\">rowMeans <- apply(express, <span class=\"code-snippet__number\">1<\/span>, function(x) mean(as.numeric(x), na.rm = T))<\/span><\/code><code><span class=\"code-snippet_outer\">express <- express[order(rowMeans, decreasing =T),]<\/span><\/code><code><span class=\"code-snippet_outer\">express <- express[!duplicated(express[, dim(express)[<span class=\"code-snippet__number\">2<\/span>]]),] <span class=\"code-snippet__meta\">#express\u7684\u6700\u540e\u4e00\u5217\u4e3agene name<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">express <- na.omit(express)<\/span><\/code><code><span class=\"code-snippet_outer\">dim(express)<\/span><\/code><\/pre>\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=\"0.11552346570397112\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_XxvrMZmSU4NEzeiaSS4Afq8gdp0OEA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2Xg9RcWsehPrEfeIlWeFA21uqVTzXxvrMZmSU4NEzeiaSS4Afq8gdp0OEA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" data-recalc-dims=\"1\"><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u5c06\u6700\u540e\u4e00\u5217\u4f5c\u4e3a\u884c\u540d<\/span><\/code><code><span class=\"code-snippet_outer\">rownames(express) <- express[,dim(express)[<span class=\"code-snippet__number\">2<\/span>]]<\/span><\/code><code><span class=\"code-snippet_outer\">#\u5220\u9664\u6700\u540e\u4e00\u5217<\/span><\/code><code><span class=\"code-snippet_outer\">express <- express[,-(dim(express)[<span class=\"code-snippet__number\">2<\/span>])]<\/span><\/code><code><span class=\"code-snippet_outer\"># \u8868\u8fbe\u77e9\u9635\uff08express\uff09\u5df2\u6784\u5efa\u597d\uff0c\u4fdd\u5b58\u5230\u6587\u4ef6<\/span><\/code><code><span class=\"code-snippet_outer\">write.csv(express, <span class=\"code-snippet__string\">\"easy_input_expr.csv\"<\/span>, quote = F)<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p powered-by=\"xiumi.us\"><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p powered-by=\"xiumi.us\" style=\"text-align: center;letter-spacing: 0.578px;font-size: 16px;margin-bottom: 0px;white-space: normal;\"><span style=\"font-size: 14px;\"><strong style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;white-space: normal;\"><em><span style=\"font-size: 20px;\">5.\u6309\u7167\u5b9e\u9a8c\u8bbe\u8ba1\u6574\u7406\u5206\u7ec4\u4fe1\u606f<\/span><\/em><\/strong><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">pdata <- pData(eset)<\/span><\/code><code><span class=\"code-snippet_outer\">i <- sapply(pdata, is.factor)<\/span><\/code><code><span class=\"code-snippet_outer\">pdata[i] <- lapply(pdata[i], as.character)<\/span><\/code><code><span class=\"code-snippet_outer\"># \u6309\u7167\u5b9e\u9a8c\u8bbe\u8ba1\uff0c\u6784\u5efa\u5206\u7ec4\u77e9\u9635<\/span><\/code><code><span class=\"code-snippet_outer\">group_list <- subset(pdata, select = title) # Sample\u7684\u5206\u7ec4\u4fe1\u606f<\/span><\/code><code><span class=\"code-snippet_outer\">group_list$condition = rep(c(<span class=\"code-snippet__string\">\"a\"<\/span>,<span class=\"code-snippet__string\">\"b\"<\/span>), each = <span class=\"code-snippet__number\">3<\/span>)<\/span><\/code><\/pre>\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=\"0.2786885245901639\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/12_HwSwrSCz9IoicAAiajTmibINwu5m7A.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgNKd5lBAsUxBPbycibvK8mjFqic8erHwSwrSCz9IoicAAiajTmibINwu5m7A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"488\" data-recalc-dims=\"1\"><\/p>\n<p><br \/><\/p>\n<p><span style=\"font-size: 14px;\">#\u5206\u7ec4\u77e9\u9635\uff08design\uff09\u5df2\u6784\u5efa\u597d<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">write.table(group_list, <span class=\"code-snippet__string\">\"easy_input_pheno.txt\"<\/span>, quote = F, sep = <span class=\"code-snippet__string\">\"t\"<\/span>, row.names = F)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p><br \/><\/p>\n<p style=\"text-align: center;letter-spacing: 0.578px;font-size: 16px;margin-bottom: 0px;white-space: normal;\"><span style=\"font-size: 14px;\"><strong style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;white-space: normal;\"><em><span style=\"font-size: 20px;\">6.\u5229\u7528limma \u5305\u8fdb\u884c\u5dee\u5f02\u5206\u6790<\/span><\/em><\/strong><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u4e0d\u505a\u5747\u4e00\u5316\u5904\u7406<\/span><\/code><code><span class=\"code-snippet_outer\">express.norm <- express<\/span><\/code><code><span class=\"code-snippet_outer\">#\u751f\u6210\u6a21\u578b\u8bbe\u8ba1\u77e9\u9635<\/span><\/code><code><span class=\"code-snippet_outer\">design <- model.matrix(~ <span class=\"code-snippet__number\">0<\/span> + factor(group_list$condition))<\/span><\/code><code><span class=\"code-snippet_outer\">#\u66ff\u6362\u5217\u540d<\/span><\/code><code><span class=\"code-snippet_outer\">colnames(design) <- levels(factor(group_list$condition))<\/span><\/code><code><span class=\"code-snippet_outer\">#\u66ff\u6362\u884c\u540d<\/span><\/code><code><span class=\"code-snippet_outer\">rownames(design) <- colnames(express.norm)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3862815884476534\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-19_\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790\/13_MUx9Ek2VO9RAJCgqylAPEh7mdjZzFA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgRgMnpxyXSRYNGIEKEcWb3SiaxMUx9Ek2VO9RAJCgqylAPEh7mdjZzFA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\"><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u6784\u5efa\u6bd4\u8f83\u77e9\u9635<\/span><\/code><code><span class=\"code-snippet_outer\">contrast.matrix <- makeContrasts(b-a, levels = design)<\/span><\/code><\/pre>\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=\"0.10649819494584838\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/14_776DUPvnLV6CicXMS8XZ0IpdvrY3mg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgdlQma2zNTGib8AghxtHmtKLTAc776DUPvnLV6CicXMS8XZ0IpdvrY3mg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" data-recalc-dims=\"1\"><\/p>\n<\/section>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u7ebf\u6027\u6a21\u578b\u62df\u5408<\/span><\/code><code><span class=\"code-snippet_outer\">fit <- lmFit(express.norm,design)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u8ba1\u7b97estimated coefficient \u548c\u6807\u51c6\u8bef\u5dee<\/span><\/code><code><span class=\"code-snippet_outer\">fit2 <- contrasts.fit(fit,contrast.matrix)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u5dee\u5f02\u5206\u6790<\/span><\/code><code><span class=\"code-snippet_outer\">fit2 <- eBayes(fit2)<\/span><\/code><code><span class=\"code-snippet_outer\">#\u63d0\u53d6\u6240\u6709\u5dee\u5f02\u57fa\u56e0\u8868\u683c\uff0c\u884c\u540d\u4e3aGene symbol,\u5217\u540d\u4e3b\u8981\u5173\u6ce8logFC,P.Value\u548cadj.P.Val\uff0c\u901a\u8fc7pvalue\u503c\u6392\u5e8f\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">x <- topTable(fit2, coef = <span class=\"code-snippet__number\">1<\/span>, n = Inf, adjust.method = <span class=\"code-snippet__string\">\"fdr\"<\/span>, sort.by = <span class=\"code-snippet__string\">\"P\"<\/span>)<\/span><\/code><\/pre>\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=\"0.1967509025270758\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/15_E7nBIlj2lym54Usv7JHb3r8rzETibw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgMnzplSYveJibVJib92xT0OoiaPSYE7nBIlj2lym54Usv7JHb3r8rzETibw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" data-recalc-dims=\"1\"><span style=\"font-size: 14px;letter-spacing: 0.578px;text-align: justify;\"> <\/span><\/p>\n<p><span style=\"font-size: 14px;\">#\u628a\u5168\u90e8\u57fa\u56e0\u7684limma\u5206\u6790\u7ed3\u679c\u4fdd\u5b58\u5230\u6587\u4ef6<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">write.csv(x, <span class=\"code-snippet__string\">\"limma.csv\"<\/span>, quote = F)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p><span style=\"font-size: 14px;\"><br \/><\/span><\/p>\n<p style=\"text-align: center;\"><span style=\"font-size: 14px;\"><strong style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;white-space: normal;\"><em><span style=\"font-size: 20px;\">7.\u7ed3\u679c\u6587\u4ef6<\/span><\/em><\/strong><\/span><\/p>\n<section powered-by=\"xiumi.us\" style=\"margin-bottom: 0px;font-size: 16px;letter-spacing: 0.578px;white-space: normal;\">\n<p style=\"margin-bottom: 0px;font-size: 16px;letter-spacing: 0.578px;white-space: normal;\"><strong><span style=\"font-size: 14px;\">1. gplTOgene.csv<\/span><\/strong><\/p>\n<p><span style=\"font-size: 14px;\">\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u63a2\u9488id\u5bf9\u5e94\u7684Gene symbol\u548centrez_id\uff0c\u7b2c\u4e00\u5217\u4e3a\u63a2\u9488ID\uff0c\u7b2c\u4e8c\u5217\u4e3aGene symbol,\u7b2c\u4e09\u5217\u4e3aentrez_id\u3002<\/span><\/p>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.5342960288808665\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-19_\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790\/16_n0ZYA6SzK0TPEjeM3hib98jHD83CMw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgFibsZoxxDNmh2Utm3icL9TO3de5n0ZYA6SzK0TPEjeM3hib98jHD83CMw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\"><\/p>\n<p><span style=\"font-size: 14px;\"><\/span><\/p>\n<p><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p style=\"letter-spacing: 0.578px;font-size: 16px;margin-bottom: 0px;white-space: normal;\"><strong><span style=\"font-size: 14px;\">2. easy_input_expr.csv<\/span><\/strong><\/p>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;\">\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u5904\u7406\u597d\u7684\u8868\u8fbe\u77e9\u9635\u6587\u4ef6\uff0c\u884c\u540d\u4e3aGene symbol,\u5217\u540d\u4e3a\u5bf9\u5e94\u7684\u6837\u672c\u540d\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.4548736462093863\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/17_JOxnV9dPEG3ibJbCv6EL8gpRdldwqg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgofLuWH5cpeAYKtj21LmKa6aKiaJOxnV9dPEG3ibJbCv6EL8gpRdldwqg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" data-recalc-dims=\"1\"><\/p>\n<p><span style=\"font-size: 14px;\"><\/span><\/p>\n<p><br \/><\/p>\n<p><span style=\"font-size: 14px;\"> <\/span><strong><span style=\"font-size: 14px;\">3. easy_input_pheno.txt<\/span><\/strong><\/p>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;\">\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u63d0\u53d6\u7684\u6837\u672c\u5206\u7ec4\u6587\u4ef6\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.17148014440433212\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-19_\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790\/18_7AwEyuKhURSmcRMhVrIsv6T23CdgSg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgPsqe0FO5pp2liaVlGZRk0AjFn7AwEyuKhURSmcRMhVrIsv6T23CdgSg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\"><\/p>\n<p><span style=\"font-size: 14px;\"><\/span><\/p>\n<p style=\"letter-spacing: 0.578px;font-size: 16px;margin-bottom: 0px;white-space: normal;\"><span style=\"font-size: 14px;\"><strong> 4. easy_input_limma.csv<\/strong><\/span><\/p>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;\">\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u901a\u8fc7limma\u5305\u8fdb\u884c\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u6587\u4ef6\uff0c\u884c\u540d\u4e3aGene symbol,\u7b2c\u4e00\u5217\u4e3alog2FC\uff0c\u7b2c\u56db\u5217\u4e3aPvalue\u503c\uff0c\u7b2c\u4e94\u5217\u4e3a\u77eb\u6b63\u540e\u7684Pvalue\u503c\u3002<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.4602888086642599\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/19_QEK18GevNlleGTVKtVeib09oLPpu8Q.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/RpJ9AibwAxrFwj9LwFf07r3uhpoeqK2XgfottWrBEHkKSwaRhV6JKw71sMQEK18GevNlleGTVKtVeib09oLPpu8Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" data-recalc-dims=\"1\"><\/p>\n<p><span style=\"font-size: 14px;\"> <\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u4eca\u5929\u5c0f\u679c\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\u5566\uff01\u5982\u679c\u5c0f\u4f19\u4f34\u6709\u5176\u4ed6\u6570\u636e\u5206\u6790\u9700\u6c42\uff0c\u53ef\u4ee5\u5c1d\u8bd5\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\uff1ahttp:\/\/www.biocloudservice.com\/home.html,\u5305\u62ec\u4e86GEO\u6570\u636e\u4e0b\u8f7d(http:\/\/www.biocloudservice.com\/371\/371.php),limma+gsva(http:\/\/www.biocloudservice.com\/371\/371.php)\u7b49\u5c0f\u5de5\u5177\uff0c\u6b22\u8fce\u5927\u5bb6\u548c\u5c0f\u679c\u4e00\u8d77\u8ba8\u8bba\u5b66\u4e60\u54c8\uff01\uff01\uff01\uff01<\/span><\/p>\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=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;font-size: 16px;\">\n<section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section data-tools=\"135\u7f16\u8f91\u5668\" data-id=\"105054\" style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;font-size: 16px;\">\n<section style=\"margin: 10px auto;text-align: center;\">\n<section style=\"padding-top: 30px;padding-bottom: 30px;background-color: rgb(242, 246, 255);border-radius: 7px;\">\n<section style=\"display: flex;justify-content: space-evenly;align-items: center;\">\n<section data-width=\"26%\" style=\"width: 150.266px;\">\n<section style=\"padding: 7px;border-radius: 15px;box-shadow: rgba(169, 187, 223, 0.45) 4px 4px 8px, rgb(255, 255, 255) -2.5px -2.5px 5px;\">\n<section data-width=\"100%\" style=\"width: 136.266px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-cropselx1=\"0\" data-cropselx2=\"136\" data-cropsely1=\"0\" data-cropsely2=\"137\" data-ratio=\"1\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-06-19_\u5982\u6b64\u7b80\u5355\u5417\uff1f\u4e00\u6587\u62ff\u634fGEO\u6570\u636e\u5e93\u82af\u7247\u6570\u636e\u4e0b\u8f7d\u53ca\u5dee\u5f02\u5206\u6790\/20_jEYQoRbKh3HUg3IGgzymibpTnmaM6Q.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwIX3hF1ZZeqvXLknM5Oq7CDG9YFpmvU1ge12vc3NvibhViceQjEYQoRbKh3HUg3IGgzymibpTnmaM6Q\/640?wx_fmt=jpeg'\" data-type=\"png\" data-w=\"430\" data-width=\"100%\" style=\"height: 137px;vertical-align: inherit;width: 137px;display: block;border-radius: 7px;\" title=\"\u5c0f\u4e91-\u5fae\u4fe1\u4e8c\u7ef4\u7801.png\" \/><\/section>\n<\/section>\n<\/section>\n<section data-width=\"62%\" style=\"width: 358.359px;\">\n<section style=\"display: inline-block;\">\n<section style=\"padding: 7px 15px;border-radius: 20px;box-shadow: rgba(169, 187, 223, 0.45) 6px 6px 8px inset, rgb(255, 255, 255) -2.5px -2.5px 5px inset;\">\n<section 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