<\/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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data={\"mp\":\"\u751f\u4fe1\u679c\",\"title\":\"\u5982\u679c\u4f60\u8fd8\u4e0d\u4f1a\u5229\u7528limma\u8fdb\u884c\u591a\u7ec4\u5dee\u5f02\u5206\u6790\uff1f\u4e0d\u614c\uff01\u8ddf\u7740\u5c0f\u679c\u4e00\u6587\u62ff\u634f\",\"time\":\"2023-07-05 19:00:29\",\"timeStamp\":\"1688554829\"};\n<\/script> \n<body><\/p>\n<div class=\"rich_media\">\n<h1 class=\"rich_media_title\" id=\"activity-name\"><a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247489796&idx=1&sn=fc72ed3b9458a9656ef1bda18183cc3c&chksm=cf7c89c1f80b00d738642d22d7b92e0474c1d23018907a817f5e4c24abaa2c8362e9bd81852c#rd\" target=\"_blank\" rel=\"noopener\">\u5982\u679c\u4f60\u8fd8\u4e0d\u4f1a\u5229\u7528limma\u8fdb\u884c\u591a\u7ec4\u5dee\u5f02\u5206\u6790\uff1f\u4e0d\u614c\uff01\u8ddf\u7740\u5c0f\u679c\u4e00\u6587\u62ff\u634f<\/a><\/h1>\n<div id=\"meta_content\" class=\"rich_media_meta_list\">\u539f\u521b <\/span>\u5c0f\u679c <\/span><a href=\"javascript:void(0);\" class=\"wx_tap_link js_wx_tap_highlight weui-wa-hotarea\" id=\"js_name\">\u751f\u4fe1\u679c <\/a><\/span>2023-07-05 19:00:29<\/em><\/div>\n<content><\/p>\n<section style=\"font-size: 16px;\">\n<section style=\"\" powered-by=\"xiumi.us\">\n<section style=\"text-align: left;\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section style=\"letter-spacing: 0.578px;\">\n<section>\n<section style=\"width: 100%;flex: 0 0 100%;\" powered-by=\"xiumi.us\">\n<section style=\"opacity: 1;width: 100%;\">\n<section powered-by=\"xiumi.us\">\n<section style=\"line-height: 1.8;\">\n<section style=\"margin-top: 10px;margin-bottom: 20px;width: 100%;\" powered-by=\"xiumi.us\">\n<section style=\"flex-flow: row nowrap;text-align: center;width: 100%;\">\n<section style=\"display: flex;justify-content: center;flex-direction: row;\">\n<section style=\"display: inline-block;width: 100%;flex: 0 0 auto;align-self: flex-start;vertical-align: top;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;border-style: solid;border-width: 1px;border-color: rgb(67, 67, 67);height: auto;box-shadow: 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-3.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\u4eca\u5929\u5c0f\u679c\u60f3\u4e3a\u5927\u5bb6\u5206\u4eab\u7684\u662f\u57fa\u4e8elimma\u5305\u8fdb\u884c\u591a\u7ec4\u5dee\u5f02\u5206\u6790<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/p>\nlimma\u5305\u5728\u8fdb\u884cGEO\u6570\u636e\u5e93mRNA\u82af\u7247\u6570\u636e\u5206\u6790\u65f6\uff0c\u4f7f\u7528\u7684\u9891\u7387\u975e\u5e38\u975e\u5e38\u9ad8\uff0c\u5f3a\u70c8\u5b89\u5229\u5c0f\u4f19\u4f34\u5b66\u4e60\u5965\uff01\u6709GEO\u6570\u636e\u5206\u6790\u9700\u6c42\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u8ddf\u7740\u5c0f\u679c\u4e00\u8d77\u6765\u5b66\u4e60\uff0c\u63a5\u4e0b\u6765\u5c0f\u679c\u5c31\u5f00\u59cb\u4eca\u5929\u7684\u5206\u4eab\u3002<\/span><\/p>\n <\/p>\n <\/span><\/p>\n1. \u5982\u4f55\u5229\u7528limma\u8fdb\u884c\u591a\u7ec4\u5dee\u5f02\u5206\u6790\uff1f<\/span><\/em><\/strong><\/p>\n\u5728\u8fdb\u884c\u8bb2\u89e3\u5982\u4f55\u8fdb\u884c\u5206\u6790\u4e4b\u524d\uff0c\u5c0f\u679c\u60f3\u4e3a\u5c0f\u4f19\u4f34\u7b80\u5355\u8bb2\u89e3\u4e00\u4e0blimma\u5305\u7684\u5206\u6790\u539f\u7406\uff0c\u8be5\u5305\u662f\u57fa\u4e8e\u7ebf\u6027\u6a21\u578b\u8fdb\u884c\u5dee\u5f02\u5206\u6790\uff0c\u5982\u4f55\u4f7f\u7528\u8be5\u5305\u8fdb\u884c\u8f6c\u5f55\u7ec4\u6570\u636e\u5dee\u5f02\u5206\u6790\uff0c\u53ef\u4ee5\u53c2\u8003\u5b98\u7f51http:\/\/bioconductor.org\/packages\/release\/bioc\/vignettes\/limma\/inst\/doc\/usersguide.pdf\u6587\u6863\u8fdb\u884c\u5b66\u4e60\uff0c\u5c0f\u679c\u5728\u8fd9\u91cc\u5c31\u4e0d\u505a\u8be6\u7ec6\u4ecb\u7ecd\u4e86\u3002<\/span>\u672c\u63a8\u6587\u53ea\u9700\u8981\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u6587\u4ef6\u548c\u6837\u672c\u5206\u7ec4\u6587\u4ef6\uff0c\u5c31\u53ef\u4ee5\u6279\u91cf\u5b8c\u6210\u591a\u7ec4\u5dee\u5f02\u5206\u6790\uff0c\u975e\u5e38\u7b80\u5355\u65b9\u4fbf\uff0c\u503c\u5f97\u5c0f\u4f19\u4f34\u4eec\u5b66\u4e60\u5965\uff01\u63a5\u4e0b\u6765\u8ddf\u7740\u5c0f\u679c\u5f00\u59cb\u4eca\u5929\u7684\u5b9e\u64cd\u5b66\u4e60\u5427\uff01<\/p>\n<\/span><\/p>\n <\/p>\n2. \u51c6\u5907\u9700\u8981\u7684R\u5305<\/span><\/em><\/strong><\/p>\nlimma\u5305\u7684\u5b89\u88c5\u76f4\u63a5\u53ef\u4ee5\u901a\u8fc7Bioconductor\u5b89\u88c5\uff0c\u5b89\u88c5\u975e\u5e38\u7b80\u5355\uff0c\u5c0f\u679c\u4e3a\u5927\u5bb6\u4e5f\u63d0\u4f9b\u7f51\u5740\uff1ahttp:\/\/bioconductor.org\/packages\/release\/bioc\/html\/limma.html\uff0c\u5982\u4e0b\uff1a<\/span><\/p>\n <\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.5379061371841155\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_mdlWgwY6KkMoSehoNZEiahT7L9uqpA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwzQ0KL9ZawI5jS9iblRGnoQYcFymdlWgwY6KkMoSehoNZEiahT7L9uqpA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n <\/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\u88c5limma\u5305<\/span><\/code><code>BiocManager::install(\"limma\"<\/span>)<\/span><\/code><code>#\u52a0\u8f7dlimma\u5305<\/span><\/code><code>library(limma)<\/span><\/code><\/pre>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/p>\n <\/p>\n3. \u6570\u636e\u51c6\u5907<\/span><\/em><\/strong><\/p>\ninput_FPKM.txt<\/span><\/p>\n#\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u6587\u4ef6\uff0c\u884c\u540d\u4e3aGene,\u5217\u4e3a\u6837\u672c\u540d.<\/span><\/p>\n <\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.27075812274368233\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_fibXa2SticqYMX98icoI8MCDmEqplA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwiaz9xzKwn5X3zr5CicicJkUsx6MUB1fibXa2SticqYMX98icoI8MCDmEqplA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<\/span><\/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<\/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\/4_mg0VckEic29fHhhLFVV352DccdeuFA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwQKGo80Hmgam94kKpZkZqljZ7qmg0VckEic29fHhhLFVV352DccdeuFA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<\/span><\/p>\n <\/p>\n <\/p>\n4. limma\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code># \u521b\u5efa\u9700\u8981\u914d\u5bf9\u6bd4\u8f83\u7684\u5217\u8868\u51fd\u6570<\/span><\/code><code>createList <- function(group=NULL<\/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># \u914d\u5bf9limma\u5dee\u5f02\u5206\u6790\u51fd\u6570<\/span><\/code><code>twoclasslimma <- function(res.path=NULL<\/span>, expr=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(expr)<\/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, \"_limma_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> pd <- data.frame(Samples=names(tmp),Group=as.character(tmp),stringsAsFactors = F)<\/span><\/code><code> design <-model.matrix(~ -1<\/span> + factor(pd$Group, levels=c(\"treatment\"<\/span>,\"control\"<\/span>))) # \u8bbe\u8ba1\u77e9\u9635\u4ec5\u5305\u542b\u4e9a\u578b\u4fe1\u606f\uff0c\u82e5\u6709\u6279\u6b21\u6548\u5e94\u8bf7\u4fee\u6539<\/span><\/code><code> colnames(design) <- c(\"treatment\"<\/span>,\"control\"<\/span>)<\/span><\/code><code> # \u5bf9\u6570\u8f6c\u6362<\/span><\/code><code> gset <- log2(expr + 1<\/span>) <\/span><\/code><code> # \u5dee\u5f02\u8868\u8fbe\u8fc7\u7a0b<\/span><\/code><code> fit <- lmFit(gset, design=design);<\/span><\/code><code> contrastsMatrix <- makeContrasts(treatment - control, levels=c(\"treatment\"<\/span>, \"control\"<\/span>))<\/span><\/code><code> fit2 <- contrasts.fit(fit, contrasts=contrastsMatrix)<\/span><\/code><code> fit2 <- eBayes(fit2, 0.01<\/span>)<\/span><\/code><code> tT <- topTable(fit2, adjust=\"fdr\"<\/span>, sort.by=\"B\"<\/span>, number=100000<\/span>)<\/span><\/code><code> tT <- subset(tT, select=c(\"logFC\"<\/span>,\"t\"<\/span>,\"B\"<\/span>,\"P.Value\"<\/span>,\"adj.P.Val\"<\/span>))<\/span><\/code><code> colnames(tT) <- c(\"log2FC\"<\/span>,\"t\"<\/span>,\"B\"<\/span>,\"PValue\"<\/span>,\"FDR\"<\/span>)<\/span><\/code><code> tT <- tT[order(tT$FDR),]<\/span><\/code><code> write.table(tT, file=outfile, row.names=T, col.names=NA, 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># \u8bfb\u53d6\u8868\u8fbe\u77e9\u9635<\/span><\/code><code>expr <- read.table(\"input_FPKM.txt\"<\/span>,sep = \"t\"<\/span>,header = T,check.names = F,stringsAsFactors = F,row.names = 1<\/span>)<\/span><\/code><code># \u8bfb\u53d6\u5206\u7ec4\u4fe1\u606f<\/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>#\u5206\u7ec4\u540d\u79f0<\/span><\/code><code>n.sub.label <- unique(subt$TCGA_Subtype) <\/span><\/code><code>#\u5206\u7ec4\u4e2a\u6570<\/span><\/code><code>n.sub <- length(table(subt$TCGA_Subtype)) <\/span><\/code><code>### \u521b\u5efa\u914d\u5bf9\u6bd4\u8f83\u7684\u5217\u8868\u4fe1\u606f<\/span><\/code><code>#\u83b7\u5f97\u5206\u7ec4\u540d<\/span><\/code><code>group <- subt$TCGA_Subtype<\/span><\/code><code>#\u901a\u8fc7\u6837\u672c\u540d\u6765\u547d\u540d<\/span><\/code><code>names(group) <- rownames(subt)<\/span><\/code><code>#\u5229\u7528createList\u51fd\u6570\u521b\u5efa\u9700\u8981\u6bd4\u8f83\u7684\u5217\u8868\u4fe1\u606f<\/span><\/code><code>complist <- createList(group=group)<\/span><\/code><code># \u5229\u7528twoclasslimma\u51fd\u6570\u8fdb\u884c\u5206\u7ec4\u5dee\u5f02\u5206\u6790\uff0c\u6240\u6709\u914d\u5bf9\u5dee\u5f02\u8868\u8fbe\u7ed3\u679c\u90fd\u4f1a\u8f93\u51fa\u5728res.path\u8def\u5f84\u4e0b\u3002<\/span><\/code><code>twoclasslimma(res.path = \".\"<\/span>,<\/span><\/code><code> expr = expr[,intersect(colnames(expr),rownames(subt))],<\/span><\/code><code> prefix = \"SKCM\"<\/span>,<\/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_limma_test_result.immune_vs_Others.txt<\/span><\/strong><\/span><\/p>\n\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u8ba1\u7b97\u7684immune\u7ec4\u4e0e\u5176\u4ed6\u5206\u7ec4\u7684\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u6587\u4ef6,\u884c\u540d\u4e3a\u57fa\u56e0\u540d\uff0c\u7b2c\u4e00\u5217\u4e3alog2FC,\u7b2c\u56db\u5217\u4e3aPvalue\u503c\uff0c\u7b2c\u4e94\u5217\u4e3aFDR(\u77eb\u6b63\u540e\u7684P\u503c)<\/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\/5_icqDhS4OxG4tTLkHa0FopxAAS6YibA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwVuImnjibkZg0wicvnSzMR6VkC6RYicqDhS4OxG4tTLkHa0FopxAAS6YibA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<\/span><\/p>\n2. SKCM_limma_test_result.keratin_vs_Others.txt<\/span><\/strong><\/span><\/p>\n\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u8ba1\u7b97\u7684keratin\u7ec4\u4e0e\u5176\u4ed6\u5206\u7ec4\u7684\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u6587\u4ef6,\u884c\u540d\u4e3a\u57fa\u56e0\u540d\uff0c\u7b2c\u4e00\u5217\u4e3alog2FC,\u7b2c\u56db\u5217\u4e3aPvalue\u503c\uff0c\u7b2c\u4e94\u5217\u4e3aFDR(\u77eb\u6b63\u540e\u7684P\u503c)<\/span><\/p>\n <\/span><\/p>\n<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\/6_jwibiciauiaUx6Lg9Yo8LOz5YXZPJg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwTpuialoFlbWOsJWT4ZSWhYXS6noWsjwibiciauiaUx6Lg9Yo8LOz5YXZPJg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<\/span><\/p>\n3. SKCM_limma_test_result.MITF-low_vs_Others.txt<\/span><\/strong><\/span><\/p>\n\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u8ba1\u7b97\u7684MITF-low\u7ec4\u4e0e\u5176\u4ed6\u5206\u7ec4\u7684\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u6587\u4ef6,\u884c\u540d\u4e3a\u57fa\u56e0\u540d\uff0c\u7b2c\u4e00\u5217\u4e3alog2FC,\u7b2c\u56db\u5217\u4e3aPvalue\u503c\uff0c\u7b2c\u4e94\u5217\u4e3aFDR(\u77eb\u6b63\u540e\u7684P\u503c).<\/span><\/p>\n <\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.2851985559566787\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_n8tH1zDlDegLOuG4jiaiaB1dlIDPew.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwsMSWZK9wZopwXVT0Mpd2DfuQfmn8tH1zDlDegLOuG4jiaiaB1dlIDPew\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<\/span><\/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,\u5305\u62ec\u4e86\u7528edgeR\u5b9e\u73b0\u591a\u7ec4\u5dee\u5f02\u5206\u6790(http:\/\/www.biocloudservice.com\/289\/289.php)\uff0cDEseq2\u5b9e\u73b0\u591a\u7ec4\u5dee\u5f02\u5206\u6790(http:\/\/www.biocloudservice.com\/287\/287.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 <\/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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data={\"mp\":\"\u751f\u4fe1\u679c\",\"title\":\"\u5982\u679c\u4f60\u8fd8\u4e0d\u4f1a\u5229\u7528limma\u8fdb\u884c\u591a\u7ec4\u5dee\u5f02\u5206\u6790\uff1f\u4e0d\u614c\uff01\u8ddf\u7740\u5c0f\u679c\u4e00\u6587\u62ff\u634f\",\"time\":\"2023-07-05 19:00:29\",\"timeStamp\":\"1688554829\"};\n<\/script> \n<body><\/p>\n<div class=\"rich_media\">\n<h1 class=\"rich_media_title\" id=\"activity-name\"><a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247489796&idx=1&sn=fc72ed3b9458a9656ef1bda18183cc3c&chksm=cf7c89c1f80b00d738642d22d7b92e0474c1d23018907a817f5e4c24abaa2c8362e9bd81852c#rd\" target=\"_blank\" rel=\"noopener\">\u5982\u679c\u4f60\u8fd8\u4e0d\u4f1a\u5229\u7528limma\u8fdb\u884c\u591a\u7ec4\u5dee\u5f02\u5206\u6790\uff1f\u4e0d\u614c\uff01\u8ddf\u7740\u5c0f\u679c\u4e00\u6587\u62ff\u634f<\/a><\/h1>\n<div id=\"meta_content\" class=\"rich_media_meta_list\">\u539f\u521b <\/span>\u5c0f\u679c <\/span><a href=\"javascript:void(0);\" class=\"wx_tap_link js_wx_tap_highlight 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1px;border-color: rgb(67, 67, 67);height: auto;box-shadow: 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-3.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\u4eca\u5929\u5c0f\u679c\u60f3\u4e3a\u5927\u5bb6\u5206\u4eab\u7684\u662f\u57fa\u4e8elimma\u5305\u8fdb\u884c\u591a\u7ec4\u5dee\u5f02\u5206\u6790<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/p>\nlimma\u5305\u5728\u8fdb\u884cGEO\u6570\u636e\u5e93mRNA\u82af\u7247\u6570\u636e\u5206\u6790\u65f6\uff0c\u4f7f\u7528\u7684\u9891\u7387\u975e\u5e38\u975e\u5e38\u9ad8\uff0c\u5f3a\u70c8\u5b89\u5229\u5c0f\u4f19\u4f34\u5b66\u4e60\u5965\uff01\u6709GEO\u6570\u636e\u5206\u6790\u9700\u6c42\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u8ddf\u7740\u5c0f\u679c\u4e00\u8d77\u6765\u5b66\u4e60\uff0c\u63a5\u4e0b\u6765\u5c0f\u679c\u5c31\u5f00\u59cb\u4eca\u5929\u7684\u5206\u4eab\u3002<\/span><\/p>\n <\/p>\n <\/span><\/p>\n1. \u5982\u4f55\u5229\u7528limma\u8fdb\u884c\u591a\u7ec4\u5dee\u5f02\u5206\u6790\uff1f<\/span><\/em><\/strong><\/p>\n\u5728\u8fdb\u884c\u8bb2\u89e3\u5982\u4f55\u8fdb\u884c\u5206\u6790\u4e4b\u524d\uff0c\u5c0f\u679c\u60f3\u4e3a\u5c0f\u4f19\u4f34\u7b80\u5355\u8bb2\u89e3\u4e00\u4e0blimma\u5305\u7684\u5206\u6790\u539f\u7406\uff0c\u8be5\u5305\u662f\u57fa\u4e8e\u7ebf\u6027\u6a21\u578b\u8fdb\u884c\u5dee\u5f02\u5206\u6790\uff0c\u5982\u4f55\u4f7f\u7528\u8be5\u5305\u8fdb\u884c\u8f6c\u5f55\u7ec4\u6570\u636e\u5dee\u5f02\u5206\u6790\uff0c\u53ef\u4ee5\u53c2\u8003\u5b98\u7f51http:\/\/bioconductor.org\/packages\/release\/bioc\/vignettes\/limma\/inst\/doc\/usersguide.pdf\u6587\u6863\u8fdb\u884c\u5b66\u4e60\uff0c\u5c0f\u679c\u5728\u8fd9\u91cc\u5c31\u4e0d\u505a\u8be6\u7ec6\u4ecb\u7ecd\u4e86\u3002<\/span>\u672c\u63a8\u6587\u53ea\u9700\u8981\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u6587\u4ef6\u548c\u6837\u672c\u5206\u7ec4\u6587\u4ef6\uff0c\u5c31\u53ef\u4ee5\u6279\u91cf\u5b8c\u6210\u591a\u7ec4\u5dee\u5f02\u5206\u6790\uff0c\u975e\u5e38\u7b80\u5355\u65b9\u4fbf\uff0c\u503c\u5f97\u5c0f\u4f19\u4f34\u4eec\u5b66\u4e60\u5965\uff01\u63a5\u4e0b\u6765\u8ddf\u7740\u5c0f\u679c\u5f00\u59cb\u4eca\u5929\u7684\u5b9e\u64cd\u5b66\u4e60\u5427\uff01<\/p>\n<\/span><\/p>\n <\/p>\n2. \u51c6\u5907\u9700\u8981\u7684R\u5305<\/span><\/em><\/strong><\/p>\nlimma\u5305\u7684\u5b89\u88c5\u76f4\u63a5\u53ef\u4ee5\u901a\u8fc7Bioconductor\u5b89\u88c5\uff0c\u5b89\u88c5\u975e\u5e38\u7b80\u5355\uff0c\u5c0f\u679c\u4e3a\u5927\u5bb6\u4e5f\u63d0\u4f9b\u7f51\u5740\uff1ahttp:\/\/bioconductor.org\/packages\/release\/bioc\/html\/limma.html\uff0c\u5982\u4e0b\uff1a<\/span><\/p>\n <\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.5379061371841155\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_mdlWgwY6KkMoSehoNZEiahT7L9uqpA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwzQ0KL9ZawI5jS9iblRGnoQYcFymdlWgwY6KkMoSehoNZEiahT7L9uqpA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n <\/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\u88c5limma\u5305<\/span><\/code><code>BiocManager::install(\"limma\"<\/span>)<\/span><\/code><code>#\u52a0\u8f7dlimma\u5305<\/span><\/code><code>library(limma)<\/span><\/code><\/pre>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n <\/p>\n <\/p>\n3. \u6570\u636e\u51c6\u5907<\/span><\/em><\/strong><\/p>\ninput_FPKM.txt<\/span><\/p>\n#\u57fa\u56e0\u8868\u8fbe\u77e9\u9635\u6587\u4ef6\uff0c\u884c\u540d\u4e3aGene,\u5217\u4e3a\u6837\u672c\u540d.<\/span><\/p>\n <\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.27075812274368233\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_fibXa2SticqYMX98icoI8MCDmEqplA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwiaz9xzKwn5X3zr5CicicJkUsx6MUB1fibXa2SticqYMX98icoI8MCDmEqplA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<\/span><\/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<\/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\/4_mg0VckEic29fHhhLFVV352DccdeuFA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwQKGo80Hmgam94kKpZkZqljZ7qmg0VckEic29fHhhLFVV352DccdeuFA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<\/span><\/p>\n <\/p>\n <\/p>\n4. limma\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code># \u521b\u5efa\u9700\u8981\u914d\u5bf9\u6bd4\u8f83\u7684\u5217\u8868\u51fd\u6570<\/span><\/code><code>createList <- function(group=NULL<\/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># \u914d\u5bf9limma\u5dee\u5f02\u5206\u6790\u51fd\u6570<\/span><\/code><code>twoclasslimma <- function(res.path=NULL<\/span>, expr=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(expr)<\/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, \"_limma_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> pd <- data.frame(Samples=names(tmp),Group=as.character(tmp),stringsAsFactors = F)<\/span><\/code><code> design <-model.matrix(~ -1<\/span> + factor(pd$Group, levels=c(\"treatment\"<\/span>,\"control\"<\/span>))) # \u8bbe\u8ba1\u77e9\u9635\u4ec5\u5305\u542b\u4e9a\u578b\u4fe1\u606f\uff0c\u82e5\u6709\u6279\u6b21\u6548\u5e94\u8bf7\u4fee\u6539<\/span><\/code><code> colnames(design) <- c(\"treatment\"<\/span>,\"control\"<\/span>)<\/span><\/code><code> # \u5bf9\u6570\u8f6c\u6362<\/span><\/code><code> gset <- log2(expr + 1<\/span>) <\/span><\/code><code> # \u5dee\u5f02\u8868\u8fbe\u8fc7\u7a0b<\/span><\/code><code> fit <- lmFit(gset, design=design);<\/span><\/code><code> contrastsMatrix <- makeContrasts(treatment - control, levels=c(\"treatment\"<\/span>, \"control\"<\/span>))<\/span><\/code><code> fit2 <- contrasts.fit(fit, contrasts=contrastsMatrix)<\/span><\/code><code> fit2 <- eBayes(fit2, 0.01<\/span>)<\/span><\/code><code> tT <- topTable(fit2, adjust=\"fdr\"<\/span>, sort.by=\"B\"<\/span>, number=100000<\/span>)<\/span><\/code><code> tT <- subset(tT, select=c(\"logFC\"<\/span>,\"t\"<\/span>,\"B\"<\/span>,\"P.Value\"<\/span>,\"adj.P.Val\"<\/span>))<\/span><\/code><code> colnames(tT) <- c(\"log2FC\"<\/span>,\"t\"<\/span>,\"B\"<\/span>,\"PValue\"<\/span>,\"FDR\"<\/span>)<\/span><\/code><code> tT <- tT[order(tT$FDR),]<\/span><\/code><code> write.table(tT, file=outfile, row.names=T, col.names=NA, 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># \u8bfb\u53d6\u8868\u8fbe\u77e9\u9635<\/span><\/code><code>expr <- read.table(\"input_FPKM.txt\"<\/span>,sep = \"t\"<\/span>,header = T,check.names = F,stringsAsFactors = F,row.names = 1<\/span>)<\/span><\/code><code># \u8bfb\u53d6\u5206\u7ec4\u4fe1\u606f<\/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>#\u5206\u7ec4\u540d\u79f0<\/span><\/code><code>n.sub.label <- unique(subt$TCGA_Subtype) <\/span><\/code><code>#\u5206\u7ec4\u4e2a\u6570<\/span><\/code><code>n.sub <- length(table(subt$TCGA_Subtype)) <\/span><\/code><code>### \u521b\u5efa\u914d\u5bf9\u6bd4\u8f83\u7684\u5217\u8868\u4fe1\u606f<\/span><\/code><code>#\u83b7\u5f97\u5206\u7ec4\u540d<\/span><\/code><code>group <- subt$TCGA_Subtype<\/span><\/code><code>#\u901a\u8fc7\u6837\u672c\u540d\u6765\u547d\u540d<\/span><\/code><code>names(group) <- rownames(subt)<\/span><\/code><code>#\u5229\u7528createList\u51fd\u6570\u521b\u5efa\u9700\u8981\u6bd4\u8f83\u7684\u5217\u8868\u4fe1\u606f<\/span><\/code><code>complist <- createList(group=group)<\/span><\/code><code># \u5229\u7528twoclasslimma\u51fd\u6570\u8fdb\u884c\u5206\u7ec4\u5dee\u5f02\u5206\u6790\uff0c\u6240\u6709\u914d\u5bf9\u5dee\u5f02\u8868\u8fbe\u7ed3\u679c\u90fd\u4f1a\u8f93\u51fa\u5728res.path\u8def\u5f84\u4e0b\u3002<\/span><\/code><code>twoclasslimma(res.path = \".\"<\/span>,<\/span><\/code><code> expr = expr[,intersect(colnames(expr),rownames(subt))],<\/span><\/code><code> prefix = \"SKCM\"<\/span>,<\/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_limma_test_result.immune_vs_Others.txt<\/span><\/strong><\/span><\/p>\n\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u8ba1\u7b97\u7684immune\u7ec4\u4e0e\u5176\u4ed6\u5206\u7ec4\u7684\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u6587\u4ef6,\u884c\u540d\u4e3a\u57fa\u56e0\u540d\uff0c\u7b2c\u4e00\u5217\u4e3alog2FC,\u7b2c\u56db\u5217\u4e3aPvalue\u503c\uff0c\u7b2c\u4e94\u5217\u4e3aFDR(\u77eb\u6b63\u540e\u7684P\u503c)<\/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\/5_icqDhS4OxG4tTLkHa0FopxAAS6YibA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwVuImnjibkZg0wicvnSzMR6VkC6RYicqDhS4OxG4tTLkHa0FopxAAS6YibA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<\/span><\/p>\n2. SKCM_limma_test_result.keratin_vs_Others.txt<\/span><\/strong><\/span><\/p>\n\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u8ba1\u7b97\u7684keratin\u7ec4\u4e0e\u5176\u4ed6\u5206\u7ec4\u7684\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u6587\u4ef6,\u884c\u540d\u4e3a\u57fa\u56e0\u540d\uff0c\u7b2c\u4e00\u5217\u4e3alog2FC,\u7b2c\u56db\u5217\u4e3aPvalue\u503c\uff0c\u7b2c\u4e94\u5217\u4e3aFDR(\u77eb\u6b63\u540e\u7684P\u503c)<\/span><\/p>\n <\/span><\/p>\n<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\/6_jwibiciauiaUx6Lg9Yo8LOz5YXZPJg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwTpuialoFlbWOsJWT4ZSWhYXS6noWsjwibiciauiaUx6Lg9Yo8LOz5YXZPJg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<\/span><\/p>\n3. SKCM_limma_test_result.MITF-low_vs_Others.txt<\/span><\/strong><\/span><\/p>\n\u8be5\u7ed3\u679c\u6587\u4ef6\u4e3a\u8ba1\u7b97\u7684MITF-low\u7ec4\u4e0e\u5176\u4ed6\u5206\u7ec4\u7684\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u6587\u4ef6,\u884c\u540d\u4e3a\u57fa\u56e0\u540d\uff0c\u7b2c\u4e00\u5217\u4e3alog2FC,\u7b2c\u56db\u5217\u4e3aPvalue\u503c\uff0c\u7b2c\u4e94\u5217\u4e3aFDR(\u77eb\u6b63\u540e\u7684P\u503c).<\/span><\/p>\n <\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.2851985559566787\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_n8tH1zDlDegLOuG4jiaiaB1dlIDPew.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyXfCyTA59YlIjHWFZ4fSjwsMSWZK9wZopwXVT0Mpd2DfuQfmn8tH1zDlDegLOuG4jiaiaB1dlIDPew\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"554\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<\/span><\/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,\u5305\u62ec\u4e86\u7528edgeR\u5b9e\u73b0\u591a\u7ec4\u5dee\u5f02\u5206\u6790(http:\/\/www.biocloudservice.com\/289\/289.php)\uff0cDEseq2\u5b9e\u73b0\u591a\u7ec4\u5dee\u5f02\u5206\u6790(http:\/\/www.biocloudservice.com\/287\/287.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 <\/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\" textvalue=\"\u5c0f\u679c\u7684\u5355\u65e5\u5c0f\u6280\u5de7DAY6\uff1a\u5982\u4f55\u5229\u7528panImmune\u8f7b\u677e\u5206\u6790\u514d\u75ab\u6d78\u6da6\uff1f\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" style=\"font-size: 14px;\" rel=\"noopener\">2 \u5c0f\u679c\u7684\u5355\u65e5\u5c0f\u6280\u5de7DAY6\uff1a\u5982\u4f55\u5229\u7528panImmune\u8f7b\u677e\u5206\u6790\u514d\u75ab\u6d78\u6da6\uff1f<\/a> <\/p>\n<a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247488458&idx=1&sn=62bd0f5561698111f46d66c681d0eaf8&chksm=cf7c830ff80b0a19e2577c9c70b473076416343b70fbc563d423257619d5abe7104ffa5ea158&scene=21#wechat_redirect\" textvalue=\"3\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" rel=\"noopener\">3<\/span><\/a> <\/span><a target=\"_blank\" 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 wxw-img\" data-cropselx1=\"0\" data-cropselx2=\"578\" data-cropsely1=\"0\" data-cropsely2=\"322\" data-galleryid=\"\" data-ratio=\"0.7193195625759417\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_oRxs73HBHUoxCtAqBPQnq1AXricRvg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxenwVZiaibuOTpj6MMDUj2LoPdS6tic40bbGQV7QyM6QOQY8EFoRxs73HBHUoxCtAqBPQnq1AXricRvg\/640?wx_fmt=png'\" data-type=\"jpeg\" data-w=\"823\" style=\"width: 578px;height: 416px;\" data-recalc-dims=\"1\"><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: 0px;font-size: 16px;letter-spacing: 0.578px;white-space: normal;caret-color: rgba(0, 0, 0, 0);\">\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 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