<\/title> \n<meta charset=\"utf-8\"> \n<meta name=\"viewport\" content=\"width=device-width,initial-scale=1.0,maximum-scale=1.0,user-scalable=0,viewport-fit=cover\"><\/p>\n<style>\n*{margin:0;padding:0}html{-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%;line-height:1.6}img{z-index:999;position:relative;max-width:100%;margin:10px 0;}body{letter-spacing:.034em}h1,h2,h3,h4,h5,h6{font-weight:400;font-size:16px}a{color:#576b95;text-decoration:none;-webkit-tap-highlight-color:rgba(0,0,0,0)}td,th{word-wrap:break-word;padding:5px 10px;border:1px solid #DDD;}table{margin-bottom:10px;border-collapse:collapse;display:table;width:100%!important;}.appmsg_skin_default .rich_media_area_primary{background-color:#fff}.appmsg_skin_default .rich_media_area_primary .weui-loadmore_line .weui-loadmore__tips{background-color:#fff}.rich_media_area_primary{padding:20px 16px 12px;background-color:#fafafa}@media (max-width:375px){.rich_media_area_primary{padding:20px 60px 15px 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Mono\",Menlo,Courier,monospace}.code-snippet__comment,.code-snippet__quote{color:#afafaf;font-style:italic}.code-snippet__keyword,.code-snippet__selector-tag,.code-snippet__subst{color:#ca7d37}.code-snippet__number,.code-snippet__literal,.code-snippet__variable,.code-snippet__template-variable,.code-snippet__tag .code-snippet__attr{color:#0e9ce5}.code-snippet__string,.code-snippet__doctag{color:#d14}.code-snippet__title,.code-snippet__section,.code-snippet__selector-id{color:#d14}.code-snippet__subst{font-weight:normal}.code-snippet__type,.code-snippet__class 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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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rgb(255, 219, 118) 6px 6px 0px;background-color: rgb(255, 255, 255);width: 100%;\">\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\u751f\u4fe1\u4ebaR\u8bed\u8a00\u5b66\u4e60\u5fc5\u5907<\/span><\/strong><\/span><\/p>\n\u7acb\u523b\u62e5\u6709\u4e00\u4e2aRstudio\u8d26\u53f7<\/span><\/strong><\/span><\/p>\n\u5f00\u542f\u5347\u7ea7\u6a21\u5f0f\u5427<\/span><\/strong><\/span><\/p>\n\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_a6w3uam8miakwvGic9hB3WxJpe4CuA-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwVynrvEB6rJh081LxbyxJP1wg9Ria6w3uam8miakwvGic9hB3WxJpe4CuA\/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<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<section style=\"display: contents;\" powered-by=\"xiumi.us\">\n<section style=\"display: contents;\">\n<section style=\"display: contents;\">\n<section style=\"height: 0px;overflow: hidden;\"> <\/span><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin: 10px 0% 8px;justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;border-left: 3px solid rgb(219, 219, 219);border-bottom-left-radius: 0px;padding-left: 8px;align-self: flex-start;flex: 0 0 auto;\">\n<section style=\"color: rgba(0, 0, 0, 0.5);text-align: justify;font-size: 14px;\" powered-by=\"xiumi.us\">\n\u5728\u8fdb\u884cGEO\u548cTCGA\u6570\u636e\u5e93\u8f6c\u5f55\u7ec4\u6570\u636e\u6316\u6398\u65f6\uff0c\u5dee\u5f02\u5206\u6790\u662f\u4e0d\u53ef\u6216\u7f3a\u7684\u4e00\u90e8\u5206\uff0c\u4e00\u822c\u8fdb\u884c\u5dee\u5f02\u5206\u6790\u7684\u4e3b\u6d41\u8f6f\u4ef6\u6709\u4e09\u6b3eDEseq2,limma,edgeR\u3002<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/p>\n\u4eca\u5929\u5c0f\u679c\u4e3a\u5927\u5bb6\u5e26\u6765\u7684\u5206\u4eab\u662f\u901a\u8fc7DEseq2<\/span>\u8fdb\u884c\u591a\u7ec4\u5dee\u5f02\u5206\u6790\uff0c \u901a\u8fc7\u8be5\u63a8\u6587\u5c06\u5b8c\u5168\u638c\u63e1\u5229\u7528DEseq2\u5305\u8fdb\u884c\u5dee\u5f02\u5206\u6790\uff0c\u503c\u5f97\u5c0f\u4f19\u4f34\u9605\u8bfb\u5b66\u4e60\u5965\uff01\u8bdd\u4e0d\u591a\u8bf4\uff0c\u548c\u5c0f\u679c\u4e00\u8d77\u5f00\u542f\u4eca\u5929\u7684\u5b66\u4e60\u4e4b\u65c5\u5427\uff01<\/span><\/p>\n<\/span><\/p>\n <\/span><\/p>\n1. \u5982\u4f55\u5b9e\u73b0DEseq2\u591a\u7ec4\u5dee\u5f02\u5206\u6790\uff1f<\/span><\/em><\/strong><\/p>\n\u8be5\u5982\u4f55\u5229\u7528DEseq2\u5b9e\u73b0\u591a\u7ec4\u5dee\u5f02\u5206\u6790\uff0c\u5176\u5b9e\u6ca1\u90a3\u4e48\u96be\uff0c\u5c0f\u4f19\u4f34\u53ea\u9700\u8981\u51c6\u5907\u597d\u57fa\u56e0reads count\u77e9\u9635\u6587\u4ef6\u548c\u6837\u672c\u5206\u7ec4\u4fe1\u606f\u6587\u4ef6\uff0c\u53ef\u4ee5\u57fa\u4e8e\u5206\u7ec4\u4fe1\u606f\u6587\u4ef6\u8fdb\u884c\u591a\u7ec4\u7684\u5dee\u5f02\u5206\u6790\uff0c\u5c0f\u4f19\u4f34\u4eec\u53ea\u9700\u8981\u638c\u63e1DEseq2 R\u5305\u53c2\u6570\u4f7f\u7528\u65b9\u6cd5\uff0c\u5c31\u53ef\u4ee5\u987a\u5229\u5feb\u901f\u7684\u8fdb\u884c\u5206\u6790\uff0c\u5c0f\u679c\u4e3a\u5927\u5bb6\u4ecb\u7ecd\u4e86\u662f\u901a\u8fc7\u6279\u91cf\u64cd\u4f5c\u7684\u65b9\u5f0f\u8fdb\u884c\u591a\u7ec4\u5dee\u5f02\u5206\u6790\uff0c\u53ea\u9700\u8981\u638c\u63e1\u57fa\u7840\u7684R\u8bed\u8a00\u77e5\u8bc6\u5c31\u53ef\u4ee5\u8fdb\u884c\u81ea\u5df1\u6570\u636e\u7684\u5904\u7406\uff0c\u5f88\u9002\u5408\u5c0f\u767d\u5965\uff0c\u90a3\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u5f00\u542f\u4eca\u5929\u7684\u5b9e\u64cd\u5427\uff01<\/span><\/p>\n <\/span><\/p>\n <\/span><\/p>\n2. \u51c6\u5907\u9700\u8981\u7684R\u5305<\/span><\/em><\/strong><\/p>\nDEseq2\u5305\u76f4\u63a5\u53ef\u4ee5\u901a\u8fc7Bioconductor \u5b89\u88c5\u5c31\u53ef\u4ee5\u7684\uff0c\u975e\u5e38\u7b80\u5355\uff0c\u5c0f\u679c\u4e3a\u5c0f\u4f19\u4f34\u4eec\u9644\u4e0a\u7f51\u5740\uff1ahttps:\/\/www.bioconductor.org\/packages\/release\/bioc\/html\/DESeq2.html<\/span><\/span><\/p>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code>#\u5b89\u88c5\u9700\u8981\u7684R\u5305<\/span><\/code><code>BiocManager::install(\"DESeq2\"<\/span>)<\/span><\/code><code>#\u8f7d\u5165\u9700\u8981\u7684R\u5305<\/span><\/code><code>library(DESeq2)<\/span><\/code><\/pre>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/p>\n <\/span><\/p>\n3. \u6570\u636e\u51c6\u5907<\/span><\/em><\/strong><\/p>\ninput_counts.txt<\/span><\/p>\n#\u57fa\u56e0count\u77e9\u9635\u6587\u4ef6,\u884c\u540d\u4e3aGene,\u5217\u4e3a\u6837\u672c\u540d\u3002<\/span><\/p>\n <\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.30324909747292417\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_cgALnsTTBBPfHHFbQGUJk2dZNOwG0Q-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwa6yMth74II903VzbTYyks4s1cgALnsTTBBPfHHFbQGUJk2dZNOwG0Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n <\/p>\ninput_subtype.txt<\/span><\/p>\n#\u6837\u672c\u5206\u7ec4\u4fe1\u606f\u6587\u4ef6\uff0c\u7b2c\u4e00\u5217\u4e3a\u6837\u672c\u540d\uff0c\u7b2c\u4e8c\u5217\u4e3a\u5206\u7ec4\u4fe1\u606f\u3002<\/span><\/p>\n <\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3935018050541516\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_gTxkxsm70zqO8MyoOFOtSAvI9OGhTw-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwpGxdNwuFicbKpXCM45ba7YTp1gTxkxsm70zqO8MyoOFOtSAvI9OGhTw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n <\/span><\/em><\/strong><\/p>\n <\/span><\/em><\/strong><\/p>\n4. DEseq2\u8fdb\u884c\u591a\u7ec4\u5dee\u5f02\u5206\u6790<\/span><\/em><\/strong><\/p>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<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>#\u8bfb\u53d6\u57fa\u56e0count\u77e9\u9635\u6587\u4ef6<\/span><\/code><code>expr <- read.table(\"input_counts.txt\"<\/span>,sep = \"t\"<\/span>,header = T,check.names = F,stringsAsFactors = F,row.names = 1<\/span>)<\/span><\/code><code># \u8bfb\u53d6\u6837\u672c\u5206\u7ec4\u4fe1\u606f\u6587\u4ef6<\/span><\/code><code>subt <- read.table(\"input_subtype.txt\"<\/span>, sep = \"t\"<\/span>, check.names = F, stringsAsFactors = F, header = T, row.names = 1<\/span>)<\/span><\/code><code># \u4e9a\u578b\u540d\u79f0<\/span><\/code><code>n.sub.label <- unique(subt$TCGA_Subtype) <\/span><\/code><code># \u4e9a\u578b\u4e2a\u6570<\/span><\/code><code>n.sub <- length(table(subt$TCGA_Subtype)) <\/span><\/code><code>#\u521b\u5efa\u914d\u5bf9\u6bd4\u8f83\u7684\u5217\u8868\u4fe1\u606f <\/span><\/code><code>group <- subt$TCGA_Subtype<\/span><\/span><\/code><code>names<\/span>(group)<\/span> <- rownames<\/span>(subt)<\/span><\/span><\/code><code># \u521b\u5efa\u9700\u8981\u914d\u5bf9\u6bd4\u8f83\u7684\u5217\u8868\u51fd\u6570,\u521b\u5efa\u4e86\u4e09\u4e2a\u5206\u7ec4\u3002<\/span><\/code><code>createList <- function<\/span>(group=NULL<\/span>)<\/span> <\/span>{<\/span><\/code><code> tumorsam <- names(group)<\/span><\/code><code> sampleList = list<\/span>()<\/span><\/code><code> treatsamList =list<\/span>()<\/span><\/code><code> treatnameList <- c()<\/span><\/code><code> ctrlnameList <- c()<\/span><\/code><code> #A-1<\/span>: \u7c7b1<\/span> vs \u5176\u4ed6<\/span><\/code><code> sampleList[[1<\/span>]] = tumorsam<\/span><\/code><code> treatsamList[[1<\/span>]] = intersect(tumorsam, names(group[group==\"immune\"<\/span>])) # \u4e9a\u578b\u540d\u79f0\u9700\u8981\u6839\u636e\u60c5\u51b5\u4fee\u6539<\/span><\/code><code> treatnameList[1<\/span>] <- \"immune\"<\/span> # \u8be5\u4e9a\u578b\u7684\u547d\u540d<\/span><\/code><code> ctrlnameList[1<\/span>] <- \"Others\"<\/span> # \u5176\u4ed6\u4e9a\u578b\u7684\u547d\u540d<\/span><\/code><code> #A-2<\/span>: \u7c7b2<\/span> vs \u5176\u4ed6<\/span><\/code><code> sampleList[[2<\/span>]] = tumorsam<\/span><\/code><code> treatsamList[[2<\/span>]] = intersect(tumorsam, names(group[group==\"keratin\"<\/span>]))<\/span><\/code><code> treatnameList[2<\/span>] <- \"keratin\"<\/span><\/span><\/code><code> ctrlnameList[2<\/span>] <- \"Others\"<\/span><\/span><\/code><code> #A-3<\/span>: \u7c7b3<\/span> vs \u5176\u4ed6<\/span><\/code><code> sampleList[[3<\/span>]] = tumorsam<\/span><\/code><code> treatsamList[[3<\/span>]] = intersect(tumorsam, names(group[group==\"MITF-low\"<\/span>]))<\/span><\/code><code> treatnameList[3<\/span>] <- \"MITF-low\"<\/span><\/span><\/code><code> ctrlnameList[3<\/span>] <- \"Others\"<\/span><\/span><\/code><code> #\u5982\u679c\u6709\u66f4\u591a\u7c7b\uff0c\u6309\u4ee5\u4e0a\u89c4\u5f8b\u7ee7\u7eed\u5199<\/span><\/code><code> return<\/span>(list<\/span>(sampleList, treatsamList, treatnameList, ctrlnameList))<\/span><\/code><code>}<\/span><\/code><code>complist <- createList(group=group)<\/span><\/code><code># \u914d\u5bf9DESeq2\u51fd\u6570<\/span><\/code><code>twoclassDESeq2 <- function(res.path=NULL<\/span>, countsTable=NULL<\/span>, prefix=NULL<\/span>, complist=NULL<\/span>, overwt=FALSE) {<\/span><\/code><code> sampleList <- complist[[1<\/span>]]<\/span><\/code><code> treatsamList <- complist[[2<\/span>]]<\/span><\/code><code> treatnameList <- complist[[3<\/span>]]<\/span><\/code><code> ctrlnameList <- complist[[4<\/span>]]<\/span><\/code><code> allsamples <- colnames(countsTable)<\/span><\/code><code> options(warn=1<\/span>)<\/span><\/code><code> for<\/span> (k in 1<\/span>:length(sampleList)) { # \u5faa\u73af\u8bfb\u53d6\u6bcf\u4e00\u6b21\u6bd4\u8f83\u7684\u5185\u5bb9<\/span><\/code><code> samples <- sampleList[[k]]<\/span><\/code><code> treatsam <- treatsamList[[k]]<\/span><\/code><code> treatname <- treatnameList[k]<\/span><\/code><code> ctrlname <- ctrlnameList[k]<\/span><\/code><code> compname <- paste(treatname, \"_vs_\"<\/span>, ctrlname, sep=\"\"<\/span>) # \u751f\u6210\u6700\u7ec8\u6587\u4ef6\u540d<\/span><\/code><code> tmp = rep(\"others\"<\/span>, times=length(allsamples))<\/span><\/code><code> names(tmp) <- allsamples<\/span><\/code><code> tmp[samples]=\"control\"<\/span><\/span><\/code><code> tmp[treatsam]=\"treatment\"<\/span><\/span><\/code><code> outfile <- file.path( res.path, paste(prefix, \"_deseq2_test_result.\"<\/span>, compname, \".txt\"<\/span>, sep=\"\"<\/span>) )<\/span><\/code><code> if<\/span> (file.exists(outfile) & (overwt==FALSE)) { # \u56e0\u4e3a\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u8f83\u6162\uff0c\u56e0\u6b64\u5982\u679c\u6587\u4ef6\u5b58\u5728\uff0c\u5728\u4e0d\u8986\u76d6\u7684\u60c5\u51b5\u4e0b\uff08overwt=F\uff09\u4e0d\u518d\u6b21\u8ba1\u7b97\u5dee\u5f02\u8868\u8fbe<\/span><\/code><code> cat(k, \":\"<\/span>, compname, \"exists and skipped;n\"<\/span>)<\/span><\/code><code> next<\/span><\/code><code> }<\/span><\/code><code> saminfo <- data.frame(\"Type\"<\/span>=tmp[samples],\"SampleID\"<\/span>=samples,stringsAsFactors = F)<\/span><\/code><code> cts <- countsTable[,samples]<\/span><\/code><code> coldata <- saminfo[samples,]<\/span><\/code><code> # \u5dee\u5f02\u8868\u8fbe\u8fc7\u7a0b\uff0c\u5177\u4f53\u53c2\u6570\u7ec6\u8282\u53ca\u8f93\u51fa\u7ed3\u679c\u89e3\u91ca\uff0c\u8bf7\u53c2\u9605\u76f8\u5173document<\/span><\/code><code> dds <- DESeqDataSetFromMatrix(countData = cts,<\/span><\/code><code> colData = coldata,<\/span><\/code><code> design = as.formula(\"~ Type\"<\/span>)) # \u8bbe\u8ba1\u77e9\u9635\u4ec5\u5305\u542b\u4e9a\u578b\u4fe1\u606f<\/span><\/code><code> dds$Type <- relevel(dds$Type,ref = \"control\"<\/span>)<\/span><\/code><code> dds <- DESeq(dds)<\/span><\/code><code> res <- results(dds, contrast=c(\"Type\"<\/span>,\"treatment\"<\/span>,\"control\"<\/span>))<\/span><\/code><code> #\u5c06\u5206\u6790\u7ed3\u679c\u8f6c\u5316\u4e3a\u6570\u636e\u6846<\/span><\/code><code>resData <- as.data.frame(res[order(res$padj),])<\/span><\/code><code> #\u5c06\u884c\u540d\u4f5c\u4e3aid\u5217<\/span><\/code><code>resData$id <- rownames(resData)<\/span><\/code><code> #\u63d0\u53d6\u60f3\u8981\u7684\u5217\u6570\u636e<\/span><\/code><code>resData <- resData[,c(\"id\"<\/span>,\"baseMean\"<\/span>,\"log2FoldChange\"<\/span>,\"lfcSE\"<\/span>,\"stat\"<\/span>,\"pvalue\"<\/span>,\"padj\"<\/span>)]<\/span><\/code><code> #\u4fee\u6539\u5217\u540d<\/span><\/code><code>colnames(resData) <- c(\"id\"<\/span>,\"baseMean\"<\/span>,\"log2FC\"<\/span>,\"lfcSE\"<\/span>,\"stat\"<\/span>,\"PValue\"<\/span>,\"FDR\"<\/span>)<\/span><\/code><code> #\u8f93\u51fa\u5230\u6587\u4ef6<\/span><\/code><code> write.table(resData, file=outfile, row.names=F, col.names=T, sep=\"t\"<\/span>, quote=F)<\/span><\/code><code> cat(k, \",\"<\/span>)<\/span><\/code><code> }<\/span><\/code><code> options(warn=0<\/span>)<\/span><\/code><code>}<\/span><\/code><code># \u5dee\u5f02\u8868\u8fbe\u5206\u6790\u8fc7\u7a0b\u6bd4\u8f83\u6162\u8bf7\u8010\u5fc3\u7b49\u5f85<\/span><\/code><code>twoclassDESeq2(res.path = \".\"<\/span>, #\u6240\u6709\u914d\u5bf9\u5dee\u5f02\u8868\u8fbe\u7ed3\u679c\u90fd\u4f1a\u8f93\u51fa\u5728res.path\u8def\u5f84\u4e0b<\/span><\/code><code> countsTable = expr[,intersect(colnames(expr),rownames(subt))],<\/span><\/code><code> prefix = \"SKCM\"<\/span>, #\u6587\u4ef6\u540d\u4ee5SKCM\u5f00\u5934<\/span><\/code><code> complist = complist,<\/span><\/code><code> overwt = F)<\/span><\/code><\/pre>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/p>\n <\/p>\n5. \u7ed3\u679c\u6587\u4ef6<\/span><\/em><\/strong><\/p>\n1. SKCM_deseq2_test_result.immune_vs_Others.txt<\/span><\/strong><\/p>\n\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u8ba1\u7b97\u7684immune\u4e0e\u5176\u4ed6\u5206\u7ec4\u7684\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u6587\u4ef6,\u7b2c\u4e00\u5217\u4e3a\u57fa\u56e0\u540d\uff0c\u7b2c\u4e09\u5217\u4e3alog2FC,\u7b2c\u516d\u5217\u4e3apvalue\u503c\uff0c\u7b2c\u4e03\u5217\u4e3aFDR\u503c(\u77eb\u6b63\u540e\u7684pvalue).<\/span><\/p>\n <\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.20938628158844766\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_gxkyoXPIibRgWc2MjCAGMG6siccTTA-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwP36c6nzyqglUygCYm7FOp8jdYEgxkyoXPIibRgWc2MjCAGMG6siccTTA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n <\/span><\/p>\n2. SKCM_deseq2_test_result.keratin_vs_Others.txt<\/span><\/strong><\/p>\n\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u8ba1\u7b97\u7684keratin\u4e0e\u5176\u4ed6\u5206\u7ec4\u7684\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u6587\u4ef6,\u7b2c\u4e00\u5217\u4e3a\u57fa\u56e0\u540d\uff0c\u7b2c\u4e09\u5217\u4e3alog2FC,\u7b2c\u516d\u5217\u4e3apvalue\u503c\uff0c\u7b2c\u4e03\u5217\u4e3aFDR\u503c(\u77eb\u6b63\u540e\u7684pvalue).<\/span><\/p>\n <\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.23826714801444043\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_tPpMX5DdlNnuprKWiaLSE2UCgia0ww-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwkaXVWO9oGfMur9QzR7LPel1hjGtPpMX5DdlNnuprKWiaLSE2UCgia0ww\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n <\/span><\/strong><\/p>\n3. SKCM_deseq2_test_result.MITF-low_vs_Others.txt<\/span><\/strong><\/p>\n\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u8ba1\u7b97\u7684MITF-low\u4e0e\u5176\u4ed6\u5206\u7ec4\u7684\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u6587\u4ef6,\u7b2c\u4e00\u5217\u4e3a\u57fa\u56e0\u540d\uff0c\u7b2c\u4e09\u5217\u4e3alog2FC,\u7b2c\u516d\u5217\u4e3apvalue\u503c\uff0c\u7b2c\u4e03\u5217\u4e3aFDR\u503c(\u77eb\u6b63\u540e\u7684pvalue).<\/span><\/p>\n <\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.21299638989169675\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_eE9tQYlJYvttNW4X0v6iayzGYlm6YQ-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwLYVsaQVtMbiaE0x6krrE91xr5yeE9tQYlJYvttNW4X0v6iayzGYlm6YQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n <\/span><\/p>\n\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\u4f7f\u7528\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u751f\u4fe1\u5206\u6790\u5c0f\u5de5\u5177\u4e91\u5e73\u53f0\uff0c\u96f6\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u975e\u5e38\u65b9\u4fbf\u5965\uff0c\u4e91\u5e73\u53f0\u7f51\u5740\u4e3a\uff1ahttp:\/\/www.biocloudservice.com\/home.html,\u4e3b\u8981\u5305\u62ecDEseq2\u5b9e\u73b0\u591a\u7ec4\u5dee\u5f02\u5206\u6790(http:\/\/www.biocloudservice.com\/287\/287.php)\uff0climma\u5b9e\u73b0\u591a\u7ec4\u5dee\u5f02\u5206\u6790(http:\/\/www.biocloudservice.com\/289\/289.php)\u7b49\u5c0f\u5de5\u5177\u6b22\u8fce\u5927\u5bb6\u548c\u5c0f\u679c\u4e00\u8d77\u8ba8\u8bba\u5b66\u4e60\u54c8\uff01\uff01\uff01\uff01<\/span><\/p>\n <\/span><\/p>\n<\/span><\/p>\n<section style=\"margin-bottom: 0px;padding-right: 1em;padding-left: 1em;font-size: 16px;letter-spacing: 0.578px;text-align: center;white-space: normal;display: inline-block;\"><span title=\"\" opera-tn-ra-cell=\"_$.pages:0.layers:0.comps:9.title1\" style=\"padding: 0.3em 0.5em;display: inline-block;border-radius: 0.5em;font-size: 14px;color: rgb(255, 255, 255);background-color: rgb(71, 193, 168);\"><\/p>\n\u5f80\u671f\u63a8\u8350 <\/p>\n<\/span><\/section>\n <\/p>\n<section style=\"margin-top: -1em;margin-bottom: 0px;padding: 20px 10px 10px;font-size: 16px;letter-spacing: 0.578px;text-align: center;white-space: normal;border-width: 1px;border-style: solid;border-color: rgb(192, 200, 209);background-color: rgb(239, 239, 239);\">\n<section powered-by=\"xiumi.us\" style=\"text-align: justify;\">\n<a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247488460&idx=1&sn=3069e8e7f85558703a8ae813375c1552&chksm=cf7c8309f80b0a1fd21e59e711c31141c96f126290f21bf78e2103d5716bdbf41acc36d6ca2a&scene=21#wechat_redirect\" textvalue=\"1\" 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rgb(255, 219, 118) 6px 6px 0px;background-color: rgb(255, 255, 255);width: 100%;\">\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\u751f\u4fe1\u4ebaR\u8bed\u8a00\u5b66\u4e60\u5fc5\u5907<\/span><\/strong><\/span><\/p>\n\u7acb\u523b\u62e5\u6709\u4e00\u4e2aRstudio\u8d26\u53f7<\/span><\/strong><\/span><\/p>\n\u5f00\u542f\u5347\u7ea7\u6a21\u5f0f\u5427<\/span><\/strong><\/span><\/p>\n\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_a6w3uam8miakwvGic9hB3WxJpe4CuA-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwVynrvEB6rJh081LxbyxJP1wg9Ria6w3uam8miakwvGic9hB3WxJpe4CuA\/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<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<section style=\"display: contents;\" powered-by=\"xiumi.us\">\n<section style=\"display: contents;\">\n<section style=\"display: contents;\">\n<section style=\"height: 0px;overflow: hidden;\"> <\/span><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin: 10px 0% 8px;justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;border-left: 3px solid rgb(219, 219, 219);border-bottom-left-radius: 0px;padding-left: 8px;align-self: flex-start;flex: 0 0 auto;\">\n<section style=\"color: rgba(0, 0, 0, 0.5);text-align: justify;font-size: 14px;\" powered-by=\"xiumi.us\">\n\u5728\u8fdb\u884cGEO\u548cTCGA\u6570\u636e\u5e93\u8f6c\u5f55\u7ec4\u6570\u636e\u6316\u6398\u65f6\uff0c\u5dee\u5f02\u5206\u6790\u662f\u4e0d\u53ef\u6216\u7f3a\u7684\u4e00\u90e8\u5206\uff0c\u4e00\u822c\u8fdb\u884c\u5dee\u5f02\u5206\u6790\u7684\u4e3b\u6d41\u8f6f\u4ef6\u6709\u4e09\u6b3eDEseq2,limma,edgeR\u3002<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/p>\n\u4eca\u5929\u5c0f\u679c\u4e3a\u5927\u5bb6\u5e26\u6765\u7684\u5206\u4eab\u662f\u901a\u8fc7DEseq2<\/span>\u8fdb\u884c\u591a\u7ec4\u5dee\u5f02\u5206\u6790\uff0c \u901a\u8fc7\u8be5\u63a8\u6587\u5c06\u5b8c\u5168\u638c\u63e1\u5229\u7528DEseq2\u5305\u8fdb\u884c\u5dee\u5f02\u5206\u6790\uff0c\u503c\u5f97\u5c0f\u4f19\u4f34\u9605\u8bfb\u5b66\u4e60\u5965\uff01\u8bdd\u4e0d\u591a\u8bf4\uff0c\u548c\u5c0f\u679c\u4e00\u8d77\u5f00\u542f\u4eca\u5929\u7684\u5b66\u4e60\u4e4b\u65c5\u5427\uff01<\/span><\/p>\n<\/span><\/p>\n <\/span><\/p>\n1. \u5982\u4f55\u5b9e\u73b0DEseq2\u591a\u7ec4\u5dee\u5f02\u5206\u6790\uff1f<\/span><\/em><\/strong><\/p>\n\u8be5\u5982\u4f55\u5229\u7528DEseq2\u5b9e\u73b0\u591a\u7ec4\u5dee\u5f02\u5206\u6790\uff0c\u5176\u5b9e\u6ca1\u90a3\u4e48\u96be\uff0c\u5c0f\u4f19\u4f34\u53ea\u9700\u8981\u51c6\u5907\u597d\u57fa\u56e0reads count\u77e9\u9635\u6587\u4ef6\u548c\u6837\u672c\u5206\u7ec4\u4fe1\u606f\u6587\u4ef6\uff0c\u53ef\u4ee5\u57fa\u4e8e\u5206\u7ec4\u4fe1\u606f\u6587\u4ef6\u8fdb\u884c\u591a\u7ec4\u7684\u5dee\u5f02\u5206\u6790\uff0c\u5c0f\u4f19\u4f34\u4eec\u53ea\u9700\u8981\u638c\u63e1DEseq2 R\u5305\u53c2\u6570\u4f7f\u7528\u65b9\u6cd5\uff0c\u5c31\u53ef\u4ee5\u987a\u5229\u5feb\u901f\u7684\u8fdb\u884c\u5206\u6790\uff0c\u5c0f\u679c\u4e3a\u5927\u5bb6\u4ecb\u7ecd\u4e86\u662f\u901a\u8fc7\u6279\u91cf\u64cd\u4f5c\u7684\u65b9\u5f0f\u8fdb\u884c\u591a\u7ec4\u5dee\u5f02\u5206\u6790\uff0c\u53ea\u9700\u8981\u638c\u63e1\u57fa\u7840\u7684R\u8bed\u8a00\u77e5\u8bc6\u5c31\u53ef\u4ee5\u8fdb\u884c\u81ea\u5df1\u6570\u636e\u7684\u5904\u7406\uff0c\u5f88\u9002\u5408\u5c0f\u767d\u5965\uff0c\u90a3\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u5f00\u542f\u4eca\u5929\u7684\u5b9e\u64cd\u5427\uff01<\/span><\/p>\n <\/span><\/p>\n <\/span><\/p>\n2. \u51c6\u5907\u9700\u8981\u7684R\u5305<\/span><\/em><\/strong><\/p>\nDEseq2\u5305\u76f4\u63a5\u53ef\u4ee5\u901a\u8fc7Bioconductor \u5b89\u88c5\u5c31\u53ef\u4ee5\u7684\uff0c\u975e\u5e38\u7b80\u5355\uff0c\u5c0f\u679c\u4e3a\u5c0f\u4f19\u4f34\u4eec\u9644\u4e0a\u7f51\u5740\uff1ahttps:\/\/www.bioconductor.org\/packages\/release\/bioc\/html\/DESeq2.html<\/span><\/span><\/p>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code>#\u5b89\u88c5\u9700\u8981\u7684R\u5305<\/span><\/code><code>BiocManager::install(\"DESeq2\"<\/span>)<\/span><\/code><code>#\u8f7d\u5165\u9700\u8981\u7684R\u5305<\/span><\/code><code>library(DESeq2)<\/span><\/code><\/pre>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/p>\n <\/span><\/p>\n3. \u6570\u636e\u51c6\u5907<\/span><\/em><\/strong><\/p>\ninput_counts.txt<\/span><\/p>\n#\u57fa\u56e0count\u77e9\u9635\u6587\u4ef6,\u884c\u540d\u4e3aGene,\u5217\u4e3a\u6837\u672c\u540d\u3002<\/span><\/p>\n <\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.30324909747292417\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_cgALnsTTBBPfHHFbQGUJk2dZNOwG0Q-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwa6yMth74II903VzbTYyks4s1cgALnsTTBBPfHHFbQGUJk2dZNOwG0Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n <\/p>\ninput_subtype.txt<\/span><\/p>\n#\u6837\u672c\u5206\u7ec4\u4fe1\u606f\u6587\u4ef6\uff0c\u7b2c\u4e00\u5217\u4e3a\u6837\u672c\u540d\uff0c\u7b2c\u4e8c\u5217\u4e3a\u5206\u7ec4\u4fe1\u606f\u3002<\/span><\/p>\n <\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3935018050541516\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_gTxkxsm70zqO8MyoOFOtSAvI9OGhTw-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwpGxdNwuFicbKpXCM45ba7YTp1gTxkxsm70zqO8MyoOFOtSAvI9OGhTw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n <\/span><\/em><\/strong><\/p>\n <\/span><\/em><\/strong><\/p>\n4. DEseq2\u8fdb\u884c\u591a\u7ec4\u5dee\u5f02\u5206\u6790<\/span><\/em><\/strong><\/p>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<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>#\u8bfb\u53d6\u57fa\u56e0count\u77e9\u9635\u6587\u4ef6<\/span><\/code><code>expr <- read.table(\"input_counts.txt\"<\/span>,sep = \"t\"<\/span>,header = T,check.names = F,stringsAsFactors = F,row.names = 1<\/span>)<\/span><\/code><code># \u8bfb\u53d6\u6837\u672c\u5206\u7ec4\u4fe1\u606f\u6587\u4ef6<\/span><\/code><code>subt <- read.table(\"input_subtype.txt\"<\/span>, sep = \"t\"<\/span>, check.names = F, stringsAsFactors = F, header = T, row.names = 1<\/span>)<\/span><\/code><code># \u4e9a\u578b\u540d\u79f0<\/span><\/code><code>n.sub.label <- unique(subt$TCGA_Subtype) <\/span><\/code><code># \u4e9a\u578b\u4e2a\u6570<\/span><\/code><code>n.sub <- length(table(subt$TCGA_Subtype)) <\/span><\/code><code>#\u521b\u5efa\u914d\u5bf9\u6bd4\u8f83\u7684\u5217\u8868\u4fe1\u606f <\/span><\/code><code>group <- subt$TCGA_Subtype<\/span><\/span><\/code><code>names<\/span>(group)<\/span> <- rownames<\/span>(subt)<\/span><\/span><\/code><code># \u521b\u5efa\u9700\u8981\u914d\u5bf9\u6bd4\u8f83\u7684\u5217\u8868\u51fd\u6570,\u521b\u5efa\u4e86\u4e09\u4e2a\u5206\u7ec4\u3002<\/span><\/code><code>createList <- function<\/span>(group=NULL<\/span>)<\/span> <\/span>{<\/span><\/code><code> tumorsam <- names(group)<\/span><\/code><code> sampleList = list<\/span>()<\/span><\/code><code> treatsamList =list<\/span>()<\/span><\/code><code> treatnameList <- c()<\/span><\/code><code> ctrlnameList <- c()<\/span><\/code><code> #A-1<\/span>: \u7c7b1<\/span> vs \u5176\u4ed6<\/span><\/code><code> sampleList[[1<\/span>]] = tumorsam<\/span><\/code><code> treatsamList[[1<\/span>]] = intersect(tumorsam, names(group[group==\"immune\"<\/span>])) # \u4e9a\u578b\u540d\u79f0\u9700\u8981\u6839\u636e\u60c5\u51b5\u4fee\u6539<\/span><\/code><code> treatnameList[1<\/span>] <- \"immune\"<\/span> # \u8be5\u4e9a\u578b\u7684\u547d\u540d<\/span><\/code><code> ctrlnameList[1<\/span>] <- \"Others\"<\/span> # \u5176\u4ed6\u4e9a\u578b\u7684\u547d\u540d<\/span><\/code><code> #A-2<\/span>: \u7c7b2<\/span> vs \u5176\u4ed6<\/span><\/code><code> sampleList[[2<\/span>]] = tumorsam<\/span><\/code><code> treatsamList[[2<\/span>]] = intersect(tumorsam, names(group[group==\"keratin\"<\/span>]))<\/span><\/code><code> treatnameList[2<\/span>] <- \"keratin\"<\/span><\/span><\/code><code> ctrlnameList[2<\/span>] <- \"Others\"<\/span><\/span><\/code><code> #A-3<\/span>: \u7c7b3<\/span> vs \u5176\u4ed6<\/span><\/code><code> sampleList[[3<\/span>]] = tumorsam<\/span><\/code><code> treatsamList[[3<\/span>]] = intersect(tumorsam, names(group[group==\"MITF-low\"<\/span>]))<\/span><\/code><code> treatnameList[3<\/span>] <- \"MITF-low\"<\/span><\/span><\/code><code> ctrlnameList[3<\/span>] <- \"Others\"<\/span><\/span><\/code><code> #\u5982\u679c\u6709\u66f4\u591a\u7c7b\uff0c\u6309\u4ee5\u4e0a\u89c4\u5f8b\u7ee7\u7eed\u5199<\/span><\/code><code> return<\/span>(list<\/span>(sampleList, treatsamList, treatnameList, ctrlnameList))<\/span><\/code><code>}<\/span><\/code><code>complist <- createList(group=group)<\/span><\/code><code># \u914d\u5bf9DESeq2\u51fd\u6570<\/span><\/code><code>twoclassDESeq2 <- function(res.path=NULL<\/span>, countsTable=NULL<\/span>, prefix=NULL<\/span>, complist=NULL<\/span>, overwt=FALSE) {<\/span><\/code><code> sampleList <- complist[[1<\/span>]]<\/span><\/code><code> treatsamList <- complist[[2<\/span>]]<\/span><\/code><code> treatnameList <- complist[[3<\/span>]]<\/span><\/code><code> ctrlnameList <- complist[[4<\/span>]]<\/span><\/code><code> allsamples <- colnames(countsTable)<\/span><\/code><code> options(warn=1<\/span>)<\/span><\/code><code> for<\/span> (k in 1<\/span>:length(sampleList)) { # \u5faa\u73af\u8bfb\u53d6\u6bcf\u4e00\u6b21\u6bd4\u8f83\u7684\u5185\u5bb9<\/span><\/code><code> samples <- sampleList[[k]]<\/span><\/code><code> treatsam <- treatsamList[[k]]<\/span><\/code><code> treatname <- treatnameList[k]<\/span><\/code><code> ctrlname <- ctrlnameList[k]<\/span><\/code><code> compname <- paste(treatname, \"_vs_\"<\/span>, ctrlname, sep=\"\"<\/span>) # \u751f\u6210\u6700\u7ec8\u6587\u4ef6\u540d<\/span><\/code><code> tmp = rep(\"others\"<\/span>, times=length(allsamples))<\/span><\/code><code> names(tmp) <- allsamples<\/span><\/code><code> tmp[samples]=\"control\"<\/span><\/span><\/code><code> tmp[treatsam]=\"treatment\"<\/span><\/span><\/code><code> outfile <- file.path( res.path, paste(prefix, \"_deseq2_test_result.\"<\/span>, compname, \".txt\"<\/span>, sep=\"\"<\/span>) )<\/span><\/code><code> if<\/span> (file.exists(outfile) & (overwt==FALSE)) { # \u56e0\u4e3a\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u8f83\u6162\uff0c\u56e0\u6b64\u5982\u679c\u6587\u4ef6\u5b58\u5728\uff0c\u5728\u4e0d\u8986\u76d6\u7684\u60c5\u51b5\u4e0b\uff08overwt=F\uff09\u4e0d\u518d\u6b21\u8ba1\u7b97\u5dee\u5f02\u8868\u8fbe<\/span><\/code><code> cat(k, \":\"<\/span>, compname, \"exists and skipped;n\"<\/span>)<\/span><\/code><code> next<\/span><\/code><code> }<\/span><\/code><code> saminfo <- data.frame(\"Type\"<\/span>=tmp[samples],\"SampleID\"<\/span>=samples,stringsAsFactors = F)<\/span><\/code><code> cts <- countsTable[,samples]<\/span><\/code><code> coldata <- saminfo[samples,]<\/span><\/code><code> # \u5dee\u5f02\u8868\u8fbe\u8fc7\u7a0b\uff0c\u5177\u4f53\u53c2\u6570\u7ec6\u8282\u53ca\u8f93\u51fa\u7ed3\u679c\u89e3\u91ca\uff0c\u8bf7\u53c2\u9605\u76f8\u5173document<\/span><\/code><code> dds <- DESeqDataSetFromMatrix(countData = cts,<\/span><\/code><code> colData = coldata,<\/span><\/code><code> design = as.formula(\"~ Type\"<\/span>)) # \u8bbe\u8ba1\u77e9\u9635\u4ec5\u5305\u542b\u4e9a\u578b\u4fe1\u606f<\/span><\/code><code> dds$Type <- relevel(dds$Type,ref = \"control\"<\/span>)<\/span><\/code><code> dds <- DESeq(dds)<\/span><\/code><code> res <- results(dds, contrast=c(\"Type\"<\/span>,\"treatment\"<\/span>,\"control\"<\/span>))<\/span><\/code><code> #\u5c06\u5206\u6790\u7ed3\u679c\u8f6c\u5316\u4e3a\u6570\u636e\u6846<\/span><\/code><code>resData <- as.data.frame(res[order(res$padj),])<\/span><\/code><code> #\u5c06\u884c\u540d\u4f5c\u4e3aid\u5217<\/span><\/code><code>resData$id <- rownames(resData)<\/span><\/code><code> #\u63d0\u53d6\u60f3\u8981\u7684\u5217\u6570\u636e<\/span><\/code><code>resData <- resData[,c(\"id\"<\/span>,\"baseMean\"<\/span>,\"log2FoldChange\"<\/span>,\"lfcSE\"<\/span>,\"stat\"<\/span>,\"pvalue\"<\/span>,\"padj\"<\/span>)]<\/span><\/code><code> #\u4fee\u6539\u5217\u540d<\/span><\/code><code>colnames(resData) <- c(\"id\"<\/span>,\"baseMean\"<\/span>,\"log2FC\"<\/span>,\"lfcSE\"<\/span>,\"stat\"<\/span>,\"PValue\"<\/span>,\"FDR\"<\/span>)<\/span><\/code><code> #\u8f93\u51fa\u5230\u6587\u4ef6<\/span><\/code><code> write.table(resData, file=outfile, row.names=F, col.names=T, sep=\"t\"<\/span>, quote=F)<\/span><\/code><code> cat(k, \",\"<\/span>)<\/span><\/code><code> }<\/span><\/code><code> options(warn=0<\/span>)<\/span><\/code><code>}<\/span><\/code><code># \u5dee\u5f02\u8868\u8fbe\u5206\u6790\u8fc7\u7a0b\u6bd4\u8f83\u6162\u8bf7\u8010\u5fc3\u7b49\u5f85<\/span><\/code><code>twoclassDESeq2(res.path = \".\"<\/span>, #\u6240\u6709\u914d\u5bf9\u5dee\u5f02\u8868\u8fbe\u7ed3\u679c\u90fd\u4f1a\u8f93\u51fa\u5728res.path\u8def\u5f84\u4e0b<\/span><\/code><code> countsTable = expr[,intersect(colnames(expr),rownames(subt))],<\/span><\/code><code> prefix = \"SKCM\"<\/span>, #\u6587\u4ef6\u540d\u4ee5SKCM\u5f00\u5934<\/span><\/code><code> complist = complist,<\/span><\/code><code> overwt = F)<\/span><\/code><\/pre>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/p>\n <\/p>\n5. \u7ed3\u679c\u6587\u4ef6<\/span><\/em><\/strong><\/p>\n1. SKCM_deseq2_test_result.immune_vs_Others.txt<\/span><\/strong><\/p>\n\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u8ba1\u7b97\u7684immune\u4e0e\u5176\u4ed6\u5206\u7ec4\u7684\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u6587\u4ef6,\u7b2c\u4e00\u5217\u4e3a\u57fa\u56e0\u540d\uff0c\u7b2c\u4e09\u5217\u4e3alog2FC,\u7b2c\u516d\u5217\u4e3apvalue\u503c\uff0c\u7b2c\u4e03\u5217\u4e3aFDR\u503c(\u77eb\u6b63\u540e\u7684pvalue).<\/span><\/p>\n <\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.20938628158844766\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_gxkyoXPIibRgWc2MjCAGMG6siccTTA-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwP36c6nzyqglUygCYm7FOp8jdYEgxkyoXPIibRgWc2MjCAGMG6siccTTA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n <\/span><\/p>\n2. SKCM_deseq2_test_result.keratin_vs_Others.txt<\/span><\/strong><\/p>\n\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u8ba1\u7b97\u7684keratin\u4e0e\u5176\u4ed6\u5206\u7ec4\u7684\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u6587\u4ef6,\u7b2c\u4e00\u5217\u4e3a\u57fa\u56e0\u540d\uff0c\u7b2c\u4e09\u5217\u4e3alog2FC,\u7b2c\u516d\u5217\u4e3apvalue\u503c\uff0c\u7b2c\u4e03\u5217\u4e3aFDR\u503c(\u77eb\u6b63\u540e\u7684pvalue).<\/span><\/p>\n <\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.23826714801444043\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_tPpMX5DdlNnuprKWiaLSE2UCgia0ww-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwkaXVWO9oGfMur9QzR7LPel1hjGtPpMX5DdlNnuprKWiaLSE2UCgia0ww\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n <\/span><\/strong><\/p>\n3. SKCM_deseq2_test_result.MITF-low_vs_Others.txt<\/span><\/strong><\/p>\n\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u8ba1\u7b97\u7684MITF-low\u4e0e\u5176\u4ed6\u5206\u7ec4\u7684\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u6587\u4ef6,\u7b2c\u4e00\u5217\u4e3a\u57fa\u56e0\u540d\uff0c\u7b2c\u4e09\u5217\u4e3alog2FC,\u7b2c\u516d\u5217\u4e3apvalue\u503c\uff0c\u7b2c\u4e03\u5217\u4e3aFDR\u503c(\u77eb\u6b63\u540e\u7684pvalue).<\/span><\/p>\n <\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.21299638989169675\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_eE9tQYlJYvttNW4X0v6iayzGYlm6YQ-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwLYVsaQVtMbiaE0x6krrE91xr5yeE9tQYlJYvttNW4X0v6iayzGYlm6YQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n <\/span><\/p>\n\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\u4f7f\u7528\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u751f\u4fe1\u5206\u6790\u5c0f\u5de5\u5177\u4e91\u5e73\u53f0\uff0c\u96f6\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u975e\u5e38\u65b9\u4fbf\u5965\uff0c\u4e91\u5e73\u53f0\u7f51\u5740\u4e3a\uff1ahttp:\/\/www.biocloudservice.com\/home.html,\u4e3b\u8981\u5305\u62ecDEseq2\u5b9e\u73b0\u591a\u7ec4\u5dee\u5f02\u5206\u6790(http:\/\/www.biocloudservice.com\/287\/287.php)\uff0climma\u5b9e\u73b0\u591a\u7ec4\u5dee\u5f02\u5206\u6790(http:\/\/www.biocloudservice.com\/289\/289.php)\u7b49\u5c0f\u5de5\u5177\u6b22\u8fce\u5927\u5bb6\u548c\u5c0f\u679c\u4e00\u8d77\u8ba8\u8bba\u5b66\u4e60\u54c8\uff01\uff01\uff01\uff01<\/span><\/p>\n <\/span><\/p>\n<\/span><\/p>\n<section style=\"margin-bottom: 0px;padding-right: 1em;padding-left: 1em;font-size: 16px;letter-spacing: 0.578px;text-align: center;white-space: normal;display: inline-block;\"><span title=\"\" opera-tn-ra-cell=\"_$.pages:0.layers:0.comps:9.title1\" style=\"padding: 0.3em 0.5em;display: inline-block;border-radius: 0.5em;font-size: 14px;color: rgb(255, 255, 255);background-color: rgb(71, 193, 168);\"><\/p>\n\u5f80\u671f\u63a8\u8350 <\/p>\n<\/span><\/section>\n <\/p>\n<section style=\"margin-top: -1em;margin-bottom: 0px;padding: 20px 10px 10px;font-size: 16px;letter-spacing: 0.578px;text-align: center;white-space: normal;border-width: 1px;border-style: solid;border-color: rgb(192, 200, 209);background-color: rgb(239, 239, 239);\">\n<section powered-by=\"xiumi.us\" style=\"text-align: justify;\">\n<a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247488460&idx=1&sn=3069e8e7f85558703a8ae813375c1552&chksm=cf7c8309f80b0a1fd21e59e711c31141c96f126290f21bf78e2103d5716bdbf41acc36d6ca2a&scene=21#wechat_redirect\" textvalue=\"1\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" rel=\"noopener\">1<\/span><\/a> <\/span><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247488460&idx=1&sn=3069e8e7f85558703a8ae813375c1552&chksm=cf7c8309f80b0a1fd21e59e711c31141c96f126290f21bf78e2103d5716bdbf41acc36d6ca2a&scene=21#wechat_redirect\" textvalue=\"PCA\u7ed8\u56fe\uff0c\u4ece\u539f\u7406\u5230\u7ed8\u56fe\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" style=\"font-size: 14px;\" rel=\"noopener\">PCA\u7ed8\u56fe\uff0c\u4ece\u539f\u7406\u5230\u7ed8\u56fe<\/a> <\/p>\n<a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247488459&idx=1&sn=d9a5d7f588994d2602cc1826c2e4f2e5&chksm=cf7c830ef80b0a1883f47601bd39bf81120fc16bc0d02f150a83f40ce52d29fbec17458830f1&scene=21#wechat_redirect\" 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href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247488458&idx=1&sn=62bd0f5561698111f46d66c681d0eaf8&chksm=cf7c830ff80b0a19e2577c9c70b473076416343b70fbc563d423257619d5abe7104ffa5ea158&scene=21#wechat_redirect\" textvalue=\"Fastp\u8f6f\u4ef6\uff1a\u5904\u7406fastq\u6587\u4ef6\u5b83\u8d85\u68d2\uff01\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" style=\"font-size: 14px;\" rel=\"noopener\">Fastp\u8f6f\u4ef6\uff1a\u5904\u7406fastq\u6587\u4ef6\u5b83\u8d85\u68d2\uff01<\/a> <\/p>\n<a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247488440&idx=1&sn=cf2e3e91652b4c8738ec8b092ede68b6&chksm=cf7c837df80b0a6b09221a3239345182772097dff21e23b36e5ed0f73b08d8c9f2e496c2f3e8&scene=21#wechat_redirect\" textvalue=\"\u9ad8\u5206\u751f\u4fe1SCI\u5e38\u7528\u7684\u80bf\u7624\u514d\u75ab\u5b66\u5355\u7ec6\u80de\u5206\u6790\u5de5\u5177\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" style=\"font-size: 14px;\" rel=\"noopener\">4 \u9ad8\u5206\u751f\u4fe1SCI\u5e38\u7528\u7684\u80bf\u7624\u514d\u75ab\u5b66\u5355\u7ec6\u80de\u5206\u6790\u5de5\u5177<\/a> <\/p>\n<a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247488459&idx=2&sn=5856888f0c879f1d2989c47da08cb064&chksm=cf7c830ef80b0a1865b8bc9efd54d6726e1b34a3f4b44bf312c19e3f1c0c38eacd6428bb6897&scene=21#wechat_redirect\" textvalue=\"\u57fa\u56e0\u7ef4\u5ea6\u592a\u9ad8\u600e\u4e48\u529e\uff1f\u65e0\u6240\u8c13\uff01PCA\u964d\u7ef4\u4f1a\u51fa\u624b\uff01\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"11\" tab=\"innerlink\" data-linktype=\"2\" style=\"font-size: 14px;\" rel=\"noopener\">5 \u57fa\u56e0\u7ef4\u5ea6\u592a\u9ad8\u600e\u4e48\u529e\uff1f\u65e0\u6240\u8c13\uff01PCA\u964d\u7ef4\u4f1a\u51fa\u624b\uff01<\/a><\/p>\n<\/section>\n<\/section>\n<\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages 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