<\/title><br \/>\n<meta charset=\"utf-8\"><br \/>\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 60px}.rich_media_area_extra{padding:0 60px 21px 60px}}@media (min-width:1024px){.rich_media_area_primary_inner,.rich_media_area_extra_inner,body{max-width:677px;margin-left:auto;margin-right:auto}.rich_media_area_primary{padding-top:32px}}.rich_media{padding:20px;overflow:hidden;}.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}@media screen and (min-width:1024px){.rich_media_area_primary_inner,.rich_media_area_extra_inner{max-width:677px;margin-left:auto;margin-right:auto}.rich_media_area_primary{padding-top:32px}}.rich_media_content{overflow:hidden;color:#333;font-size:17px;word-wrap:break-word;-webkit-hyphens:auto;-ms-hyphens:auto;hyphens:auto;text-align:justify;position:relative;z-index:0}.rich_media_content *{max-width:100%!important;box-sizing:border-box!important;-webkit-box-sizing:border-box!important;word-wrap:break-word!important}.rich_media_content p{clear:both;min-height:1em}.rich_media_content em{font-style:italic}.rich_media_content fieldset{min-width:0}.rich_media_content .list-paddingleft-1,.rich_media_content .list-paddingleft-2,.rich_media_content .list-paddingleft-3{padding-left:2.2em}.rich_media_content .list-paddingleft-1 .list-paddingleft-2,.rich_media_content .list-paddingleft-2 .list-paddingleft-2,.rich_media_content .list-paddingleft-3 .list-paddingleft-2{padding-left:30px}.rich_media_content .list-paddingleft-1{padding-left:1.2em}.rich_media_content .list-paddingleft-3{padding-left:3.2em}.rich_media_content .code-snippet,.rich_media_content .code-snippet__fix{max-width:1000%!important}.rich_media_content .code-snippet *,.rich_media_content .code-snippet__fix *{max-width:1000%!important}.rich_media_title{font-size:22px;line-height:1.4;margin-bottom:13px;padding-bottom:13px;border-bottom:1px solid #e7e7eb;}@supports(-webkit-overflow-scrolling:touch){.rich_media_title{font-weight:700}}.rich_media_meta{display:inline-block;vertical-align:middle;padding:0 0 10px 0;font-size:15px;-webkit-tap-highlight-color:rgba(0,0,0,0)}.rich_media_meta.icon_appmsg_tag{margin-right:0px}.rich_media_meta.meta_tag_text{margin-right:0}.rich_media_meta_list em{font-style:normal}.rich_media_meta_text{color:#a5a5a5;}p{margin:0;}.msgBox{margin-top:20px;padding-top:20px;padding-left:50px;overflow:hidden;border-top:2px dashed #09a2ff;}.msg{padding-top:7px;clear:both;}.msgBody{float:right;width:100%;margin-left:55px;padding-bottom:15px;border-bottom:1px dashed #e0e0e0;}.userHeadImg{float:left;margin-left:-50px;}.userHeadImg img{width:40px;height:40px;margin-right:10px;border-radius:3px;}.userName{color:#888888;line-height:24px;font-size:14px;margin:5px 0 5px 0;height:24px;}.replyBody,.autherBody{color:#565656;font-size:15px;}.replyIcon{border-left:4px solid #33ab01;margin-right:5px;}.ad{text-decoration:none;color:#d6d4d4;font-size:12px;}.msgBodyReply{padding-top:5px;}.userName span{float:right;color:#afafaf;font-size:14px;}code{text-align:left;font-size:14px;display:block;white-space:pre;display:-webkit-box;display:-webkit-flex;display:flex;position:relative;}.code-snippet__fix{font-size:14px;margin:10px 0;display:block;color:#333;position:relative;background-color:rgba(0,0,0,0.03);border:1px solid #f0f0f0;border-radius:2px;display:-webkit-box;display:-webkit-flex;display:flex;padding-left:25px;line-height:26px}.code-snippet__fix code{text-align:left;font-size:14px;display:block;white-space:pre;display:-webkit-box;display:-webkit-flex;display:flex;position:relative;font-family:Consolas,\"Liberation 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 .code-snippet__title{color:#0e9ce5}.code-snippet__tag,.code-snippet__name,.code-snippet__attribute{color:#0e9ce5;font-weight:normal}.code-snippet__regexp,.code-snippet__link{color:#ca7d37}.code-snippet__symbol,.code-snippet__bullet{color:#d14}.code-snippet__built_in,.code-snippet__builtin-name{color:#ca7d37}.code-snippet__meta{color:#afafaf}.code-snippet__deletion{background:#fdd}.code-snippet__addition{background:#dfd}.code-snippet__emphasis{font-style:italic}.code-snippet__strong{font-weight:bold}.account_avatar{width:40px;height:40px;padding:0;}.account_info{display:-webkit-box;display:-webkit-flex;display:flex;-webkit-box-align:center;-webkit-align-items:center;padding:20px 0;align-items:center}.flex_bd{padding-left:14px;}.account_nickname{display:inline-block;vertical-align:middle;line-height:1.2;color:#576b95;font-size:14px}.account_desc{overflow:hidden;text-overflow:ellipsis;display:-webkit-box;-webkit-box-orient:vertical;-webkit-line-clamp:1;color:rgba(0,0,0,0.3);font-size:14px;line-height:1.2;padding-top:.4em}.msg_source_url{text-align:left;word-break:break-all;margin-top:20px;}.msg_source_url a{padding-right:10px;}.msg_source_url .url_text{color:#a8a8a8;}.video-desc{font-size:14px;margin-top:15px;color:#6c6c6c;}.msg_source_url{text-align:left;}.original_primary_card_tips{color:rgba(0,0,0,0.3);line-height:1.4;font-size:15px;}.weui-flex__item{margin-bottom:20px;padding:20px 16px;margin-top:16px;line-height:1.4;align-items:center;background-color:#f7f7f7;border-radius:8px;position:relative;}.original_primary_desc{color:rgba(0,0,0,0.5);font-size:14px;padding-top:4px;width:auto;overflow:hidden;text-overflow:ellipsis;}.msgBodyReplyList{border-top:1px solid #e1e1e1;margin-top:10px;}.msgBodyReplyListTop{border-top:0;}.reply_like_num{float:right;font-size:14px;color:#c7c7c7;}.msgData{margin-top:20px;color:#626262;}.msgData span{font-size:14px;padding-right:15px;}.msgData .likes{float:right;padding-right:0;}.js_text_content p{font-size:18px;}.rich_media_meta_link{font-size:15px;}blockquote {padding-left: 10px;border-left: 3px solid #dbdbdb;color: rgba(0,0,0,0.5);font-size: 15px;padding-top: 4px;margin: 1em 0;}.video_iframe{width:500px;height:400px;}.blockquote_info{color:#b5b5b5;margin-top:10px;}#copyright_logo{color:#bdbdbd;}.rich_media_meta_list{margin-bottom:10px;}.reprint{background:#efefef;border-radius:5px;padding:8px;color:#1f1f1f;}.reprint a{word-break:break-all;}.topic{color:#8e8e8e;background:#f7f7f7;border-radius:5px;padding:10px 8px;}.topic a{padding-right:5px;}.topic p{margin-bottom:5px;}\n<\/style>\n<link href=\"https:\/\/www.juyifx.cn\/config\/css\/wxArticle.css\" rel=\"stylesheet\"\/>\n<\/head><script>\nvar data={\"mp\":\"\u751f\u4fe1\u679c\",\"title\":\"GEO2R\u5206\u6790R\u4ee3\u7801\u5b66\u4e60\u4e4b\u5dee\u5f02\u5206\u6790\",\"time\":\"2022-11-11 19:00:41\",\"timeStamp\":\"1668164441\"};\n<\/script><br \/>\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=2247483741&idx=1&sn=6360648cb09cc838b7d6256a4cc029da&chksm=cf7c9198f80b188e96d0a4d207521bb361bc1f6c612dd43ced95854757f25b77924578ff220f#rd\" target=\"_blank\" rel=\"noopener\">GEO2R\u5206\u6790R\u4ee3\u7801\u5b66\u4e60\u4e4b\u5dee\u5f02\u5206\u6790<\/a><\/h1>\n<div id=\"meta_content\" class=\"rich_media_meta_list\"><span id=\"copyright_logo\" class=\"wx_tap_link js_wx_tap_highlight rich_media_meta icon_appmsg_tag appmsg_title_tag weui-wa-hotarea\">\u539f\u521b <\/span><span class=\"rich_media_meta rich_media_meta_text\">\u5c0f\u679c <\/span><span class=\"rich_media_meta rich_media_meta_nickname\" id=\"profileBt\"><a href=\"javascript:void(0);\" class=\"wx_tap_link js_wx_tap_highlight weui-wa-hotarea\" id=\"js_name\">\u751f\u4fe1\u679c <\/a><\/span><em id=\"publish_time\" class=\"rich_media_meta rich_media_meta_text\">2022-11-11 19:00:41<\/em><\/div>\n<p><content><\/p>\n<div class=\"topic\">\n<p>\u6536\u5f55\u4e8e\u8bdd\u9898<\/p>\n<p><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2655932655410184193#wechat_redirect\" title=\"\u4ee3\u7801\" target=\"_blank\" rel=\"noopener\">#\u4ee3\u7801<\/a><\/p>\n<\/div>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.18518518518518517\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_YHrH5kBzN1unDT7eHqLtdZO1vwdtrw-42.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/zcicibWZessAxZibD6iaowp2Zv5dgyZQqBVAac9npnibJvGYo1ZFiafpiayXgbaYHrH5kBzN1unDT7eHqLtdZO1vwdtrw\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<section style=\"box-sizing: border-box;font-size: 16px;\">\n<section style=\"box-sizing: border-box;font-size: 16px;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;background-color: rgba(255, 255, 255, 0.83);align-self: flex-start;flex: 0 0 auto;box-sizing: border-box;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;padding: 28px 28px 7px;align-self: flex-start;flex: 0 0 auto;background-color: rgb(255, 248, 248);box-sizing: border-box;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: -25px;margin-bottom: 10px;transform: translate3d(-25px, 0px, 0px);box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 1px;border-color: rgb(207, 65, 61);min-width: 5%;max-width: 100%;height: auto;padding: 11px;box-sizing: border-box;\">\n<section style=\"margin-top: -10px;margin-bottom: -10px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: justify;box-sizing: border-box;\">\n<p style=\"white-space: normal;box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">GEO2R<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;max-width: 100%;flex: 0 0 auto;height: auto;align-self: flex-end;box-sizing: border-box;\">\n<section style=\"transform: perspective(0px);-webkit-transform: perspective(0px);-moz-transform: perspective(0px);-o-transform: perspective(0px);transform-style: flat;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"transform: translate3d(-8px, 0px, 0px) rotateX(180deg);-webkit-transform: translate3d(-8px, 0px, 0px) rotateX(180deg);-moz-transform: translate3d(-8px, 0px, 0px) rotateX(180deg);-o-transform: translate3d(-8px, 0px, 0px) rotateX(180deg);box-sizing: border-box;\">\n<section style=\"display: inline-block;width: 18px;height: 18px;vertical-align: top;overflow: hidden;background-color: rgb(207, 65, 61);box-sizing: border-box;\">\n<section style=\"text-align: justify;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\">\u4ee5GSE70493\u4e3a\u4f8b\u8fdb\u884cGEO2R\u5206\u6790\u6240\u4f7f\u7528R\u4ee3\u7801\u7684\u5b66\u4e60\uff1a<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># Version info: R 3.2.3, Biobase 2.30.0, GEOquery 2.40.0, limma 3.26.8<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\">#\u4ecb\u7ecd\u4f7f\u7528\u7684\u8f6f\u4ef6\u7684\u7248\u672c\uff0c\u4f8b\u5982R\u662f\u7248\u672c\u662f3.2.3\uff0cBiobase\u7684\u7248\u672c\u662f2.30.0, GEOquery\u7684\u7248\u672c\u662f2.40.0, limma \u7684\u7248\u672c\u662f3.26.8\u3002<\/p>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># Differential expression analysis with limma<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">library(GEOquery)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">library(limma)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">library(umap)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u5904\u8bf4\u660e\u4f7f\u7528limma\u8fdb\u884c\u5dee\u5f02\u8868\u8fbe\u5206\u6790\uff0c\u9700\u8981\u52a0\u8f7d\u7684\u4e00\u4e9bR\u5305\uff0c\u5305\u62ecGEOquery\uff0climma\uff0cumap\u3002<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># load series and platform data from GEO<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">gset <- getGEO(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"GSE70493\"<\/span>, GSEMatrix =<span class=\"code-snippet__literal\" style=\"box-sizing: border-box;\">TRUE<\/span>, AnnotGPL=<span class=\"code-snippet__literal\" style=\"box-sizing: border-box;\">FALSE<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\" style=\"box-sizing: border-box;\">if<\/span> (<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">length<\/span>(gset) > <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>) idx <- grep(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"GPL17586\"<\/span>, <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">attr<\/span>(gset, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"names\"<\/span>)) <span class=\"code-snippet__keyword\" style=\"box-sizing: border-box;\">else<\/span> idx <- 1<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">gset <- gset[[idx]]<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u4e0b\u8f7dGEO\u6570\u636e\u96c6\uff0c\u6570\u636e\u96c6\u540d\u79f0\u4e3agset<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># make proper column names to match toptable<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">fvarLabels(gset) <- make.names(fvarLabels(gset))<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u751f\u6210gset\u6570\u636e\u96c6\u7684\u5217\u540d\uff0c\u7528\u5230\u4e86make.names\u51fd\u6570\uff0c\u76ee\u7684\u662f\u4e3a\u4e86\u5b9a\u4e49\u6709\u6548\u7684\u540d\u79f0<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># group membership for all samples<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">gsms <- <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"111010111101100000111110011010001000001010000011110111100100101\"<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">sml <- strsplit(gsms, split=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"\"<\/span>)[[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>]]<\/span><\/code><\/pre>\n<\/section>\n<section style=\"box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u5bf9\u6570\u636e\u96c6\u4e2d\u6240\u6709\u7684\u6837\u672c\u8fdb\u884c\u6210\u5458\u5173\u7cfb\u5206\u6790 \uff0c\u9996\u5148\u662f\u5b9a\u4e49\u4e86\u4e00\u4e2a\u7ec4\uff0c\u7136\u540e\u4f7f\u7528\u5b57\u7b26\u4e32\u53bb\u8fdb\u884c\u5206\u5272\u5e76\u8fdb\u884c\u63d0\u53d6\uff0c\u5176\u4e2d\u7684[[1]]\uff0c\u8868\u793a\u63d0\u53d6\u67d0\u4e2a\u5217\u8868\u4e2d\u7b2c\u4e00\u4e2a\u5b50\u8868\u4e2d\u7684\u6240\u6709\u5143\u7d20\uff0c\u4e00\u822c\u6211\u4eec\u63d0\u53d6\u5217\u8868\u5176\u4e2d\u7684\u5143\u7d20\u5bf9\u8c61 \u5c3d\u91cf\u91c7\u7528[[]]\u76f4\u63a5\u63d0\u53d6\uff0c\u4e0d\u5bb9\u6613\u51fa\u9519\u3002<\/p>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># log2 transformation<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">ex <- exprs(gset)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">qx <- <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">as.numeric<\/span>(quantile(ex, <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0.<\/span>, <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0.25<\/span>, <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0.5<\/span>, <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0.75<\/span>, <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0.99<\/span>, <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1.0<\/span>), na.rm=<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">T<\/span>))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">LogC <- (qx[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">5<\/span>] > <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">100<\/span>) ||<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">(qx[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">6<\/span>]-qx[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>] > <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">50<\/span> && qx[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>] > <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__keyword\" style=\"box-sizing: border-box;\">if<\/span> (LogC) { ex[which(ex <= <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0<\/span>)] <- <span class=\"code-snippet__literal\" style=\"box-sizing: border-box;\">NaN<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">exprs(gset) <- log2(ex) }<\/span><\/code><\/pre>\n<\/section>\n<section style=\"box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u5bf9\u8868\u8fbe\u77e9\u9635ex\u8fdb\u884clog2 \u5bf9\u6570\u503c\u8f6c\u6362\uff0c\u901a\u5e38\u4f7f\u7528limma\u5904\u7406\u65f6\uff0c\u9700\u8981\u7ecf\u8fc7log2\u540e\u7684\u77e9\u9635\u4f5c\u4e3a\u8868\u8fbe\u77e9\u9635\u8f93\u5165\u3002<\/p>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># assign samples to groups and set up design matrix<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">gs <- factor(sml)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">groups <- make.names(<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"control\"<\/span>,<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"treat\"<\/span>))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">levels(gs) <- groups<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">gset$group <- gs<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">design <- model.matrix(~group + <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0<\/span>, gset)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">colnames(design) <- levels(gs)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">fit <- lmFit(gset, design) <span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># fit linear model<\/span><\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u5bf9\u6837\u672c\u8fdb\u884c\u5206\u7ec4\uff0c\u8fdb\u884c\u8868\u8fbe\u77e9\u9635\u8bbe\u8ba1<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># set up contrasts of interest and recalculate model coefficients<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">cts <- paste(groups[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>], groups[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>], sep=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"-\"<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">cont.matrix <- makeContrasts(contrasts=cts, levels=design)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">fit2 <- contrasts.fit(fit, cont.matrix)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u5efa\u7acb\u6bd4\u5bf9\u5173\u7cfb\u5e76\u91cd\u65b0\u8ba1\u7b97\u6a21\u578b\u56de\u5f52\u7cfb\u6570 \uff0c\u5177\u4f53\u7528\u5230\u7684\u51fd\u6570\u6709paste\uff0cmakeContrast\u7b49<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># compute statistics and table of top significant genes<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">fit2 <- eBayes(fit2, <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0.01<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">tT <- topTable(fit2, adjust=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"fdr\"<\/span>, sort.by=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"B\"<\/span>, number=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">250<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">tT <- subset(tT, select=<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"ID\"<\/span>,<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"adj.P.Val\"<\/span>,<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"P.Value\"<\/span>,<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"t\"<\/span>,<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"B\"<\/span>,<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"logFC\"<\/span>,<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"SPOT_ID\"<\/span>))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">write.table(tT, file=stdout(), row.names=<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">F<\/span>, sep=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"t\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u7edf\u8ba1\u5dee\u5f02\u663e\u8457\u7684\u57fa\u56e0\uff0c\u8fd9\u91cc\u7528\u5230\u4e86topTable\u51fd\u6570\uff0c\u901a\u8fc7fdr\u7684\u65b9\u6cd5\u8fdb\u884c\u77eb\u6b63\u6392\u5e8f\uff0c\u7b5b\u9009\u4e86250\u4e2a\u5dee\u5f02\u57fa\u56e0\u3002<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\"><br \/><\/p>\n<section style=\"box-sizing: border-box;font-size: 16px;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: stretch;flex: 0 0 auto;background-color: rgb(226, 91, 91);min-width: 5%;max-width: 100%;height: auto;padding-top: 5px;padding-right: 9px;padding-left: 20px;box-sizing: border-box;\">\n<section style=\"text-align: justify;color: rgb(255, 255, 255);box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">\u626b\u7801\u5173\u6ce8\u6211\u4eec<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;max-width: 100%;flex: 0 0 auto;height: auto;align-self: stretch;box-sizing: border-box;\">\n<section style=\"box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 0px;height: 0px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 38px 0px 0px 19px;border-color: rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgb(226, 91, 91);box-sizing: border-box;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 20px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: 37%;align-self: center;flex: 0 0 auto;height: auto;box-sizing: border-box;\">\n<section style=\"text-align: center;margin-top: 10px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;width: 90%;height: auto;box-sizing: border-box;\"><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\/2_89OwvlQm3aO2ML1v1qDzHNWAic9Tcg-4.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/zcicibWZessAwMHt5r1zOwBibker7jibV7yMuXX4P2dGIZhJQMKztBmhgNtxr89OwvlQm3aO2ML1v1qDzHNWAic9Tcg\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"344\" style=\"vertical-align: middle;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 57%;align-self: center;flex: 0 0 auto;height: auto;box-sizing: border-box;\">\n<section style=\"text-align: right;margin-bottom: 4px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"color: rgb(238, 216, 190);box-sizing: border-box;\">\n<p style=\"box-sizing: border-box;\">shengxinguoer<\/p>\n<\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: -4px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: right;color: rgb(226, 91, 91);font-size: 23px;line-height: 1.1;box-sizing: border-box;\">\n<p style=\"box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">\u751f\u4fe1\u679c<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<\/section>\n<section style=\"text-align: center;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: right;box-sizing: border-box;\">\n<p style=\"box-sizing: border-box;\">\u751f\u4fe1\u786c\u6838\u77e5\u8bc6\u89e3\u7b54<\/p>\n<p style=\"box-sizing: border-box;\">\u548c\u5c0f\u679c\u4e00\u8d77\u5b66\u751f\u4fe1<\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"display: none;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<p><\/content>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>GEO2R\u5206\u6790R\u4ee3\u7801\u5b66\u4e60\u4e4b\u5dee\u5f02\u5206\u6790 \u539f\u521b \u5c0f\u679c \u751f\u4fe1\u679c […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/48950"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=48950"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/48950\/revisions"}],"predecessor-version":[{"id":48955,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/48950\/revisions\/48955"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=48950"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=48950"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=48950"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}

{"id":48950,"date":"2024-06-15T20:08:25","date_gmt":"2024-06-15T12:08:25","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=48950"},"modified":"2024-06-15T20:08:25","modified_gmt":"2024-06-15T12:08:25","slug":"geo2r%e5%88%86%e6%9e%90r%e4%bb%a3%e7%a0%81%e5%ad%a6%e4%b9%a0%e4%b9%8b%e5%b7%ae%e5%bc%82%e5%88%86%e6%9e%90-2","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=48950","title":{"rendered":"GEO2R\u5206\u6790R\u4ee3\u7801\u5b66\u4e60\u4e4b\u5dee\u5f02\u5206\u6790"},"content":{"rendered":"

\n
\n<\/title><br \/>\n<meta charset=\"utf-8\"><br \/>\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 60px}.rich_media_area_extra{padding:0 60px 21px 60px}}@media (min-width:1024px){.rich_media_area_primary_inner,.rich_media_area_extra_inner,body{max-width:677px;margin-left:auto;margin-right:auto}.rich_media_area_primary{padding-top:32px}}.rich_media{padding:20px;overflow:hidden;}.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}@media screen and (min-width:1024px){.rich_media_area_primary_inner,.rich_media_area_extra_inner{max-width:677px;margin-left:auto;margin-right:auto}.rich_media_area_primary{padding-top:32px}}.rich_media_content{overflow:hidden;color:#333;font-size:17px;word-wrap:break-word;-webkit-hyphens:auto;-ms-hyphens:auto;hyphens:auto;text-align:justify;position:relative;z-index:0}.rich_media_content *{max-width:100%!important;box-sizing:border-box!important;-webkit-box-sizing:border-box!important;word-wrap:break-word!important}.rich_media_content p{clear:both;min-height:1em}.rich_media_content em{font-style:italic}.rich_media_content fieldset{min-width:0}.rich_media_content .list-paddingleft-1,.rich_media_content .list-paddingleft-2,.rich_media_content .list-paddingleft-3{padding-left:2.2em}.rich_media_content .list-paddingleft-1 .list-paddingleft-2,.rich_media_content .list-paddingleft-2 .list-paddingleft-2,.rich_media_content .list-paddingleft-3 .list-paddingleft-2{padding-left:30px}.rich_media_content .list-paddingleft-1{padding-left:1.2em}.rich_media_content .list-paddingleft-3{padding-left:3.2em}.rich_media_content .code-snippet,.rich_media_content .code-snippet__fix{max-width:1000%!important}.rich_media_content .code-snippet *,.rich_media_content .code-snippet__fix *{max-width:1000%!important}.rich_media_title{font-size:22px;line-height:1.4;margin-bottom:13px;padding-bottom:13px;border-bottom:1px solid #e7e7eb;}@supports(-webkit-overflow-scrolling:touch){.rich_media_title{font-weight:700}}.rich_media_meta{display:inline-block;vertical-align:middle;padding:0 0 10px 0;font-size:15px;-webkit-tap-highlight-color:rgba(0,0,0,0)}.rich_media_meta.icon_appmsg_tag{margin-right:0px}.rich_media_meta.meta_tag_text{margin-right:0}.rich_media_meta_list em{font-style:normal}.rich_media_meta_text{color:#a5a5a5;}p{margin:0;}.msgBox{margin-top:20px;padding-top:20px;padding-left:50px;overflow:hidden;border-top:2px dashed #09a2ff;}.msg{padding-top:7px;clear:both;}.msgBody{float:right;width:100%;margin-left:55px;padding-bottom:15px;border-bottom:1px dashed #e0e0e0;}.userHeadImg{float:left;margin-left:-50px;}.userHeadImg img{width:40px;height:40px;margin-right:10px;border-radius:3px;}.userName{color:#888888;line-height:24px;font-size:14px;margin:5px 0 5px 0;height:24px;}.replyBody,.autherBody{color:#565656;font-size:15px;}.replyIcon{border-left:4px solid #33ab01;margin-right:5px;}.ad{text-decoration:none;color:#d6d4d4;font-size:12px;}.msgBodyReply{padding-top:5px;}.userName span{float:right;color:#afafaf;font-size:14px;}code{text-align:left;font-size:14px;display:block;white-space:pre;display:-webkit-box;display:-webkit-flex;display:flex;position:relative;}.code-snippet__fix{font-size:14px;margin:10px 0;display:block;color:#333;position:relative;background-color:rgba(0,0,0,0.03);border:1px solid #f0f0f0;border-radius:2px;display:-webkit-box;display:-webkit-flex;display:flex;padding-left:25px;line-height:26px}.code-snippet__fix code{text-align:left;font-size:14px;display:block;white-space:pre;display:-webkit-box;display:-webkit-flex;display:flex;position:relative;font-family:Consolas,\"Liberation 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 .code-snippet__title{color:#0e9ce5}.code-snippet__tag,.code-snippet__name,.code-snippet__attribute{color:#0e9ce5;font-weight:normal}.code-snippet__regexp,.code-snippet__link{color:#ca7d37}.code-snippet__symbol,.code-snippet__bullet{color:#d14}.code-snippet__built_in,.code-snippet__builtin-name{color:#ca7d37}.code-snippet__meta{color:#afafaf}.code-snippet__deletion{background:#fdd}.code-snippet__addition{background:#dfd}.code-snippet__emphasis{font-style:italic}.code-snippet__strong{font-weight:bold}.account_avatar{width:40px;height:40px;padding:0;}.account_info{display:-webkit-box;display:-webkit-flex;display:flex;-webkit-box-align:center;-webkit-align-items:center;padding:20px 0;align-items:center}.flex_bd{padding-left:14px;}.account_nickname{display:inline-block;vertical-align:middle;line-height:1.2;color:#576b95;font-size:14px}.account_desc{overflow:hidden;text-overflow:ellipsis;display:-webkit-box;-webkit-box-orient:vertical;-webkit-line-clamp:1;color:rgba(0,0,0,0.3);font-size:14px;line-height:1.2;padding-top:.4em}.msg_source_url{text-align:left;word-break:break-all;margin-top:20px;}.msg_source_url a{padding-right:10px;}.msg_source_url .url_text{color:#a8a8a8;}.video-desc{font-size:14px;margin-top:15px;color:#6c6c6c;}.msg_source_url{text-align:left;}.original_primary_card_tips{color:rgba(0,0,0,0.3);line-height:1.4;font-size:15px;}.weui-flex__item{margin-bottom:20px;padding:20px 16px;margin-top:16px;line-height:1.4;align-items:center;background-color:#f7f7f7;border-radius:8px;position:relative;}.original_primary_desc{color:rgba(0,0,0,0.5);font-size:14px;padding-top:4px;width:auto;overflow:hidden;text-overflow:ellipsis;}.msgBodyReplyList{border-top:1px solid #e1e1e1;margin-top:10px;}.msgBodyReplyListTop{border-top:0;}.reply_like_num{float:right;font-size:14px;color:#c7c7c7;}.msgData{margin-top:20px;color:#626262;}.msgData span{font-size:14px;padding-right:15px;}.msgData .likes{float:right;padding-right:0;}.js_text_content p{font-size:18px;}.rich_media_meta_link{font-size:15px;}blockquote {padding-left: 10px;border-left: 3px solid #dbdbdb;color: rgba(0,0,0,0.5);font-size: 15px;padding-top: 4px;margin: 1em 0;}.video_iframe{width:500px;height:400px;}.blockquote_info{color:#b5b5b5;margin-top:10px;}#copyright_logo{color:#bdbdbd;}.rich_media_meta_list{margin-bottom:10px;}.reprint{background:#efefef;border-radius:5px;padding:8px;color:#1f1f1f;}.reprint a{word-break:break-all;}.topic{color:#8e8e8e;background:#f7f7f7;border-radius:5px;padding:10px 8px;}.topic a{padding-right:5px;}.topic p{margin-bottom:5px;}\n<\/style>\n<link href=\"https:\/\/www.juyifx.cn\/config\/css\/wxArticle.css\" rel=\"stylesheet\"\/>\n<\/head><script>\nvar data={\"mp\":\"\u751f\u4fe1\u679c\",\"title\":\"GEO2R\u5206\u6790R\u4ee3\u7801\u5b66\u4e60\u4e4b\u5dee\u5f02\u5206\u6790\",\"time\":\"2022-11-11 19:00:41\",\"timeStamp\":\"1668164441\"};\n<\/script><br \/>\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=2247483741&idx=1&sn=6360648cb09cc838b7d6256a4cc029da&chksm=cf7c9198f80b188e96d0a4d207521bb361bc1f6c612dd43ced95854757f25b77924578ff220f#rd\" target=\"_blank\" rel=\"noopener\">GEO2R\u5206\u6790R\u4ee3\u7801\u5b66\u4e60\u4e4b\u5dee\u5f02\u5206\u6790<\/a><\/h1>\n<div id=\"meta_content\" class=\"rich_media_meta_list\"><span id=\"copyright_logo\" class=\"wx_tap_link js_wx_tap_highlight rich_media_meta icon_appmsg_tag appmsg_title_tag weui-wa-hotarea\">\u539f\u521b <\/span><span class=\"rich_media_meta rich_media_meta_text\">\u5c0f\u679c <\/span><span class=\"rich_media_meta rich_media_meta_nickname\" id=\"profileBt\"><a href=\"javascript:void(0);\" class=\"wx_tap_link js_wx_tap_highlight weui-wa-hotarea\" id=\"js_name\">\u751f\u4fe1\u679c <\/a><\/span><em id=\"publish_time\" class=\"rich_media_meta rich_media_meta_text\">2022-11-11 19:00:41<\/em><\/div>\n<p><content><\/p>\n<div class=\"topic\">\n<p>\u6536\u5f55\u4e8e\u8bdd\u9898<\/p>\n<p><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2655932655410184193#wechat_redirect\" title=\"\u4ee3\u7801\" target=\"_blank\" rel=\"noopener\">#\u4ee3\u7801<\/a><\/p>\n<\/div>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.18518518518518517\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_YHrH5kBzN1unDT7eHqLtdZO1vwdtrw-42.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/zcicibWZessAxZibD6iaowp2Zv5dgyZQqBVAac9npnibJvGYo1ZFiafpiayXgbaYHrH5kBzN1unDT7eHqLtdZO1vwdtrw\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<section style=\"box-sizing: border-box;font-size: 16px;\">\n<section style=\"box-sizing: border-box;font-size: 16px;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;background-color: rgba(255, 255, 255, 0.83);align-self: flex-start;flex: 0 0 auto;box-sizing: border-box;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;padding: 28px 28px 7px;align-self: flex-start;flex: 0 0 auto;background-color: rgb(255, 248, 248);box-sizing: border-box;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: -25px;margin-bottom: 10px;transform: translate3d(-25px, 0px, 0px);box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 1px;border-color: rgb(207, 65, 61);min-width: 5%;max-width: 100%;height: auto;padding: 11px;box-sizing: border-box;\">\n<section style=\"margin-top: -10px;margin-bottom: -10px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: justify;box-sizing: border-box;\">\n<p style=\"white-space: normal;box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">GEO2R<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;max-width: 100%;flex: 0 0 auto;height: auto;align-self: flex-end;box-sizing: border-box;\">\n<section style=\"transform: perspective(0px);-webkit-transform: perspective(0px);-moz-transform: perspective(0px);-o-transform: perspective(0px);transform-style: flat;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"transform: translate3d(-8px, 0px, 0px) rotateX(180deg);-webkit-transform: translate3d(-8px, 0px, 0px) rotateX(180deg);-moz-transform: translate3d(-8px, 0px, 0px) rotateX(180deg);-o-transform: translate3d(-8px, 0px, 0px) rotateX(180deg);box-sizing: border-box;\">\n<section style=\"display: inline-block;width: 18px;height: 18px;vertical-align: top;overflow: hidden;background-color: rgb(207, 65, 61);box-sizing: border-box;\">\n<section style=\"text-align: justify;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\">\u4ee5GSE70493\u4e3a\u4f8b\u8fdb\u884cGEO2R\u5206\u6790\u6240\u4f7f\u7528R\u4ee3\u7801\u7684\u5b66\u4e60\uff1a<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># Version info: R 3.2.3, Biobase 2.30.0, GEOquery 2.40.0, limma 3.26.8<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\">#\u4ecb\u7ecd\u4f7f\u7528\u7684\u8f6f\u4ef6\u7684\u7248\u672c\uff0c\u4f8b\u5982R\u662f\u7248\u672c\u662f3.2.3\uff0cBiobase\u7684\u7248\u672c\u662f2.30.0, GEOquery\u7684\u7248\u672c\u662f2.40.0, limma \u7684\u7248\u672c\u662f3.26.8\u3002<\/p>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># Differential expression analysis with limma<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">library(GEOquery)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">library(limma)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">library(umap)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u5904\u8bf4\u660e\u4f7f\u7528limma\u8fdb\u884c\u5dee\u5f02\u8868\u8fbe\u5206\u6790\uff0c\u9700\u8981\u52a0\u8f7d\u7684\u4e00\u4e9bR\u5305\uff0c\u5305\u62ecGEOquery\uff0climma\uff0cumap\u3002<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># load series and platform data from GEO<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">gset <- getGEO(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"GSE70493\"<\/span>, GSEMatrix =<span class=\"code-snippet__literal\" style=\"box-sizing: border-box;\">TRUE<\/span>, AnnotGPL=<span class=\"code-snippet__literal\" style=\"box-sizing: border-box;\">FALSE<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\" style=\"box-sizing: border-box;\">if<\/span> (<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">length<\/span>(gset) > <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>) idx <- grep(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"GPL17586\"<\/span>, <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">attr<\/span>(gset, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"names\"<\/span>)) <span class=\"code-snippet__keyword\" style=\"box-sizing: border-box;\">else<\/span> idx <- 1<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">gset <- gset[[idx]]<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u4e0b\u8f7dGEO\u6570\u636e\u96c6\uff0c\u6570\u636e\u96c6\u540d\u79f0\u4e3agset<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># make proper column names to match toptable<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">fvarLabels(gset) <- make.names(fvarLabels(gset))<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u751f\u6210gset\u6570\u636e\u96c6\u7684\u5217\u540d\uff0c\u7528\u5230\u4e86make.names\u51fd\u6570\uff0c\u76ee\u7684\u662f\u4e3a\u4e86\u5b9a\u4e49\u6709\u6548\u7684\u540d\u79f0<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># group membership for all samples<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">gsms <- <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"111010111101100000111110011010001000001010000011110111100100101\"<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">sml <- strsplit(gsms, split=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"\"<\/span>)[[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>]]<\/span><\/code><\/pre>\n<\/section>\n<section style=\"box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u5bf9\u6570\u636e\u96c6\u4e2d\u6240\u6709\u7684\u6837\u672c\u8fdb\u884c\u6210\u5458\u5173\u7cfb\u5206\u6790 \uff0c\u9996\u5148\u662f\u5b9a\u4e49\u4e86\u4e00\u4e2a\u7ec4\uff0c\u7136\u540e\u4f7f\u7528\u5b57\u7b26\u4e32\u53bb\u8fdb\u884c\u5206\u5272\u5e76\u8fdb\u884c\u63d0\u53d6\uff0c\u5176\u4e2d\u7684[[1]]\uff0c\u8868\u793a\u63d0\u53d6\u67d0\u4e2a\u5217\u8868\u4e2d\u7b2c\u4e00\u4e2a\u5b50\u8868\u4e2d\u7684\u6240\u6709\u5143\u7d20\uff0c\u4e00\u822c\u6211\u4eec\u63d0\u53d6\u5217\u8868\u5176\u4e2d\u7684\u5143\u7d20\u5bf9\u8c61 \u5c3d\u91cf\u91c7\u7528[[]]\u76f4\u63a5\u63d0\u53d6\uff0c\u4e0d\u5bb9\u6613\u51fa\u9519\u3002<\/p>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># log2 transformation<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">ex <- exprs(gset)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">qx <- <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">as.numeric<\/span>(quantile(ex, <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0.<\/span>, <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0.25<\/span>, <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0.5<\/span>, <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0.75<\/span>, <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0.99<\/span>, <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1.0<\/span>), na.rm=<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">T<\/span>))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">LogC <- (qx[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">5<\/span>] > <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">100<\/span>) ||<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">(qx[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">6<\/span>]-qx[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>] > <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">50<\/span> && qx[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>] > <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__keyword\" style=\"box-sizing: border-box;\">if<\/span> (LogC) { ex[which(ex <= <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0<\/span>)] <- <span class=\"code-snippet__literal\" style=\"box-sizing: border-box;\">NaN<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">exprs(gset) <- log2(ex) }<\/span><\/code><\/pre>\n<\/section>\n<section style=\"box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u5bf9\u8868\u8fbe\u77e9\u9635ex\u8fdb\u884clog2 \u5bf9\u6570\u503c\u8f6c\u6362\uff0c\u901a\u5e38\u4f7f\u7528limma\u5904\u7406\u65f6\uff0c\u9700\u8981\u7ecf\u8fc7log2\u540e\u7684\u77e9\u9635\u4f5c\u4e3a\u8868\u8fbe\u77e9\u9635\u8f93\u5165\u3002<\/p>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># assign samples to groups and set up design matrix<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">gs <- factor(sml)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">groups <- make.names(<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"control\"<\/span>,<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"treat\"<\/span>))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">levels(gs) <- groups<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">gset$group <- gs<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">design <- model.matrix(~group + <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0<\/span>, gset)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">colnames(design) <- levels(gs)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">fit <- lmFit(gset, design) <span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># fit linear model<\/span><\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u5bf9\u6837\u672c\u8fdb\u884c\u5206\u7ec4\uff0c\u8fdb\u884c\u8868\u8fbe\u77e9\u9635\u8bbe\u8ba1<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># set up contrasts of interest and recalculate model coefficients<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">cts <- paste(groups[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>], groups[<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>], sep=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"-\"<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">cont.matrix <- makeContrasts(contrasts=cts, levels=design)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">fit2 <- contrasts.fit(fit, cont.matrix)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u5efa\u7acb\u6bd4\u5bf9\u5173\u7cfb\u5e76\u91cd\u65b0\u8ba1\u7b97\u6a21\u578b\u56de\u5f52\u7cfb\u6570 \uff0c\u5177\u4f53\u7528\u5230\u7684\u51fd\u6570\u6709paste\uff0cmakeContrast\u7b49<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># compute statistics and table of top significant genes<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">fit2 <- eBayes(fit2, <span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0.01<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">tT <- topTable(fit2, adjust=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"fdr\"<\/span>, sort.by=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"B\"<\/span>, number=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">250<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">tT <- subset(tT, select=<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"ID\"<\/span>,<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"adj.P.Val\"<\/span>,<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"P.Value\"<\/span>,<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"t\"<\/span>,<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"B\"<\/span>,<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"logFC\"<\/span>,<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"SPOT_ID\"<\/span>))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">write.table(tT, file=stdout(), row.names=<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">F<\/span>, sep=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"t\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u7edf\u8ba1\u5dee\u5f02\u663e\u8457\u7684\u57fa\u56e0\uff0c\u8fd9\u91cc\u7528\u5230\u4e86topTable\u51fd\u6570\uff0c\u901a\u8fc7fdr\u7684\u65b9\u6cd5\u8fdb\u884c\u77eb\u6b63\u6392\u5e8f\uff0c\u7b5b\u9009\u4e86250\u4e2a\u5dee\u5f02\u57fa\u56e0\u3002<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\"><br \/><\/p>\n<section style=\"box-sizing: border-box;font-size: 16px;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: stretch;flex: 0 0 auto;background-color: rgb(226, 91, 91);min-width: 5%;max-width: 100%;height: auto;padding-top: 5px;padding-right: 9px;padding-left: 20px;box-sizing: border-box;\">\n<section style=\"text-align: justify;color: rgb(255, 255, 255);box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">\u626b\u7801\u5173\u6ce8\u6211\u4eec<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;max-width: 100%;flex: 0 0 auto;height: auto;align-self: stretch;box-sizing: border-box;\">\n<section style=\"box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 0px;height: 0px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 38px 0px 0px 19px;border-color: rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgb(226, 91, 91);box-sizing: border-box;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 20px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: 37%;align-self: center;flex: 0 0 auto;height: auto;box-sizing: border-box;\">\n<section style=\"text-align: center;margin-top: 10px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;width: 90%;height: auto;box-sizing: border-box;\"><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\/2_89OwvlQm3aO2ML1v1qDzHNWAic9Tcg-4.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/zcicibWZessAwMHt5r1zOwBibker7jibV7yMuXX4P2dGIZhJQMKztBmhgNtxr89OwvlQm3aO2ML1v1qDzHNWAic9Tcg\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"344\" style=\"vertical-align: middle;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 57%;align-self: center;flex: 0 0 auto;height: auto;box-sizing: border-box;\">\n<section style=\"text-align: right;margin-bottom: 4px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"color: rgb(238, 216, 190);box-sizing: border-box;\">\n<p style=\"box-sizing: border-box;\">shengxinguoer<\/p>\n<\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: -4px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: right;color: rgb(226, 91, 91);font-size: 23px;line-height: 1.1;box-sizing: border-box;\">\n<p style=\"box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">\u751f\u4fe1\u679c<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<\/section>\n<section style=\"text-align: center;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: right;box-sizing: border-box;\">\n<p style=\"box-sizing: border-box;\">\u751f\u4fe1\u786c\u6838\u77e5\u8bc6\u89e3\u7b54<\/p>\n<p style=\"box-sizing: border-box;\">\u548c\u5c0f\u679c\u4e00\u8d77\u5b66\u751f\u4fe1<\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"display: none;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<p><\/content>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>GEO2R\u5206\u6790R\u4ee3\u7801\u5b66\u4e60\u4e4b\u5dee\u5f02\u5206\u6790 \u539f\u521b \u5c0f\u679c \u751f\u4fe1\u679c […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/48950"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=48950"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/48950\/revisions"}],"predecessor-version":[{"id":48955,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/48950\/revisions\/48955"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=48950"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=48950"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=48950"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}