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#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 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solid #e1e1e1;margin-top:10px;}.msgBodyReplyListTop{border-top:0;}.reply_like_num{float:right;font-size:14px;color:#c7c7c7;}.msgData{margin-top:20px;color:#626262;}.msgData span{font-size:14px;padding-right:15px;}.msgData .likes{float:right;padding-right:0;}.js_text_content p{font-size:18px;}.rich_media_meta_link{font-size:15px;}blockquote {padding-left: 10px;border-left: 3px solid #dbdbdb;color: rgba(0,0,0,0.5);font-size: 15px;padding-top: 4px;margin: 1em 0;}.video_iframe{width:500px;height:400px;}.blockquote_info{color:#b5b5b5;margin-top:10px;}#copyright_logo{color:#bdbdbd;}.rich_media_meta_list{margin-bottom:10px;}.reprint{background:#efefef;border-radius:5px;padding:8px;color:#1f1f1f;}.reprint a{word-break:break-all;}.topic{color:#8e8e8e;background:#f7f7f7;border-radius:5px;padding:10px 8px;}.topic a{padding-right:5px;}.topic p{margin-bottom:5px;}\n<\/style>\n<link href=\"https:\/\/www.juyifx.cn\/config\/css\/wxArticle.css\" rel=\"stylesheet\"\/>\n<\/head><script>\nvar 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title=\"\u751f\u4fe1\u7ed8\u56fe\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u7ed8\u56fe<\/a><\/p>\n<\/div>\n<p data-mpa-powered-by=\"yiban.io\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u8fd1\u5e74\u6765\u968f\u7740\u8d28\u8c31\u4eea\u5668\u7684\u53d1\u5c55\uff0c\u86cb\u767d\u8d28\u7ec4\u5b66\u53d6\u5f97\u4e86\u957f\u8db3\u8fdb\u6b65\uff0c\u5728\u86cb\u767d\u8d28\u7ec4\u5b66\u6108\u52a0\u706b\u70ed\u7684\u4eca\u5929\uff0c\u8fd8\u4e0d\u8d76\u7d27\u5b66\u4e60\u86cb\u767d\u8d28\u7ec4\u7684\u5206\u6790\u65b9\u6cd5\uff1f\u597d\u7684\uff0c\u4eca\u5929\u5c31\u8ba9\u5c0f\u679c\u624b\u628a\u624b\u6559\u4f60\u5982\u4f55\u4f7f\u7528\u86cb\u767d\u8d28\u7ec4\u5206\u6790\u8f6f\u4ef6\u5305DEP\u5427\uff01<\/span><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">1.\u5206\u6790\u6982\u8ff0<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u8f6f\u4ef6\u5305DEP\u63d0\u4f9b\u4e86\u4e00\u4e2a\u96c6\u6210\u7684\u5206\u6790\u5de5\u4f5c\u6d41\u7a0b\uff0c\u7528\u4e8e\u5bf9\u5dee\u5f02\u86cb\u767d\u8d28\u8868\u8fbe\u6216\u5dee\u5f02\u5bcc\u96c6\u7684\u8d28\u8c31\u6cd5\u86cb\u767d\u8d28\u7ec4\u5b66\u6570\u636e\u8fdb\u884c\u53ef\u9760\u548c\u53ef\u91cd\u590d\u7684\u5206\u6790\u3002<\/span><span style=\"text-align: center;font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/span><\/p>\n<p style=\"text-align: left;\"><span style=\"font-size: 14px;letter-spacing: 0.034em;text-align: justify;\"><em style=\"letter-spacing: 0.578px;white-space: normal;color: rgb(178, 178, 178);\"><span style=\"font-size: 13px;text-decoration: underline;\">\u516c\u4f17\u53f7\u540e\u53f0\u56de\u590d\u201c111″,\u9886\u53d6\u4ee3\u7801\uff0c\u4ee3\u7801\u7f16\u53f7\uff1a231011<\/span><\/em><\/span><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">2.\u5b89\u88c5\u4ee5\u53ca\u52a0\u8f7dR\u5305<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">if<\/span> (!requireNamespace(<span class=\"code-snippet__string\">\"BiocManager\"<\/span>, quietly=<span class=\"code-snippet__keyword\">TRUE<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"BiocManager\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::install(<span class=\"code-snippet__string\">\"DEP\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">library(<span class=\"code-snippet__string\">\"DEP\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">3.\u4ea4\u4e92\u5f0f\u4f7f\u7528\uff08\u53ef\u9009\uff09<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u8be5\u8f6f\u4ef6\u5305\u5305\u542bshiny\u7684\u5e94\u7528\u7a0b\u5e8f\uff0c\u5b83\u5141\u8bb8\u4e0b\u9762\u63cf\u8ff0\u7684\u6574\u4e2a\u5de5\u4f5c\u6d41\u7a0b\u7684\u4ea4\u4e92\u5f0f\u5206\u6790\u3002\u8fd9\u4e9b\u5e94\u7528\u7a0b\u5e8f\u7279\u522b\u9002\u7528\u4e8e\u6709\u9650\u6216\u6ca1\u6709 R \u7ecf\u9a8c\u7684\u7528\u6237\u3002\u76ee\u524d\uff0c\u6709\u4e24\u79cd\u4e0d\u540c\u7684\u5e94\u7528\u7a0b\u5e8f\u3002\u4e00\u4e2a\u7528\u4e8e\u57fa\u4e8e\u65e0\u6807\u7b7e\u5b9a\u91cf(LFQ)\u7684\u5206\u6790(\u6765\u81ea MaxQuant \u7684\u8f93\u51fa) \uff0c\u53e6\u4e00\u4e2a\u7528\u4e8e\u57fa\u4e8e\u4e32\u8054\u8d28\u91cf\u6807\u7b7e(TMT)\u7684\u5206\u6790(\u6765\u81ea IsobarQuant \u7684\u8f93\u51fa)\u3002\u8981\u8fd0\u884c\u8fd9\u4e9b\u5e94\u7528\u7a0b\u5e8f\uff0c\u53ea\u9700\u8fd0\u884c\u4ee5\u4e0b\u547d\u4ee4:<\/span><br \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"apache\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7528\u4e8e LFQ \u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">run_app<\/span>(<span class=\"code-snippet__string\">\"LFQ\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7528\u4e8e TMT \u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">run_app<\/span>(<span class=\"code-snippet__string\">\"TMT\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">4.\u5dee\u5f02\u8868\u8fbe\u5206\u6790<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u6211\u4eec\u5206\u6790\u4e86\u6cdb\u7d20-\u86cb\u767d\u8d28\u76f8\u4e92\u4f5c\u7528\u7684\u86cb\u767d\u8d28\u7ec4\u5b66\u6570\u636e\u96c6(Zhang et al. Mol Cell 2017)\u3002\u539f\u59cb\u8d28\u8c31\u6570\u636e\u9996\u5148\u4f7f\u7528 MaxQuant (Cox and Mann, Nat Biotech 2007)\u8fdb\u884c\u5206\u6790\uff0c\u7ecf\u8fc7\u5206\u6790\u4e4b\u540e\u5f97\u5230\u7684\u201c proteininGroups.txt\u201d\u6587\u4ef6\u7528\u4f5c\u4e0b\u6e38\u5206\u6790\u7684\u8f93\u5165\u3002<\/span><\/p>\n<p><strong>4.1 \u6837\u54c1\u6570\u636e\u96c6<\/strong>\uff1a<span style=\"letter-spacing: 0.034em;font-size: 14px;\">Ubiquitin interactors<\/span><\/p>\n<p><strong>4.2 \u5bfc\u5165\u6570\u636e<\/strong><\/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<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<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=\"powershell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u5bfc\u5165\u7528\u4e8e\u6570\u636e\u5904\u7406\u7684\u8f6f\u4ef6\u5305\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(<span class=\"code-snippet__string\">\"dplyr\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u8fd9\u91cc\u6211\u4eec\u4f7f\u7528\u8f6f\u4ef6\u5305\u81ea\u5e26\u7684\u6570\u636e\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">data<\/span> <- UbiLength<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u6211\u4eec\u7b5b\u9009\u6c61\u67d3\u86cb\u767d\u8d28\u548c\u8bf1\u9975\u6570\u636e\u5e93\u5339\u914d\u7ed3\u679c\uff0c\u5b83\u4eec\u5206\u522b\u7531\u201cPotential.contaminants\u201d\u548c\u201cReverse\u201d\u5217\u4e2d\u7684\u201c +\u201d\u8868\u793a<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">data<\/span> <- <span class=\"code-snippet__keyword\">filter<\/span>(<span class=\"code-snippet__keyword\">data<\/span>, Reverse != <span class=\"code-snippet__string\">\"+\"<\/span>, Potential.contaminant != <span class=\"code-snippet__string\">\"+\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">The data.frame has the following dimensions:<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">dim(<span class=\"code-snippet__keyword\">data<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## [1] 2941 23<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">The data.frame has the following column names:<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">colnames(<span class=\"code-snippet__keyword\">data<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.15462962962962962\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/1_WMGDdw7aFnDURJdmibJaTDXOIBqrVw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZOia2vAdicnKibuEy40EbJljZGu1PWMGDdw7aFnDURJdmibJaTDXOIBqrVw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" \/><\/p>\n<p><strong>4.3\u6570\u636e\u51c6\u5907<\/strong><\/p>\n<p><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u6211\u4eec\u786e\u8ba4\u6570\u636e\u96c6\u662f\u5426\u5177\u6709\u552f\u4e00\u7684 Uniprot \u6807\u8bc6\u7b26<\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"powershell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u5148\u5224\u65ad\u6570\u636e\u96c6\u662f\u5426\u6709\u91cd\u590d\u7684\u57fa\u56e0\u540d?<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">data<\/span><span class=\"code-snippet__variable\">$Gene<\/span>.names %>% duplicated() %>% any()<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.09597523219814241\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/2_7fdiaDWw1la4NLzGD9LjQe64axjOMg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZbxlY7KfrO7Tko8SeYpCe5Ea9K7fdiaDWw1la4NLzGD9LjQe64axjOMg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"646\" \/><\/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=\"powershell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u5236\u4f5c\u4e00\u4e2a\u91cd\u590d\u57fa\u56e0\u540d\u79f0\u7684\u8868\u683c\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">data<\/span> %>% group_by(Gene.names) %>% summarize(frequency = n()) %>%<\/span><\/code><code><span class=\"code-snippet_outer\">arrange(desc(frequency)) %>% <span class=\"code-snippet__keyword\">filter<\/span>(frequency > <span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.8529411764705882\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/3_kEglJiaqibJnmsBPHAI12d54WpdpnQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZvuWVc3yPAaMSGKUP8GWpbNicgmakEglJiaqibJnmsBPHAI12d54WpdpnQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"612\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"powershell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u4e3a\u4e86\u8fdb\u4e00\u6b65\u5206\u6790\uff0c\u8fd9\u4e9b\u86cb\u767d\u8d28\u5fc5\u987b\u5f97\u5230\u552f\u4e00\u7684\u540d\u79f0\u3002\u6b64\u5916\uff0c\u4e00\u4e9b\u86cb\u767d\u8d28\u6ca1\u6709\u6ce8\u91ca\u7684\u57fa\u56e0\u540d\u79f0\uff0c\u5bf9\u4e8e\u8fd9\u4e9b\uff0c\u6211\u4eec\u5c06\u4f7f\u7528 Uniprot ID<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">data_unique <- make_unique(<span class=\"code-snippet__keyword\">data<\/span>, <span class=\"code-snippet__string\">\"Gene.names\"<\/span>, <span class=\"code-snippet__string\">\"Protein.IDs\"<\/span>, delim = <span class=\"code-snippet__string\">\";\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># Are there any duplicated names?<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">data<\/span><span class=\"code-snippet__variable\">$name<\/span> %>% duplicated() %>% any()<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.24675324675324675\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/4_ZIdlrGmicBEcusby0q2KHDjTdBS76g.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZzXXQKzT8WbZRHgWto4KxPiaNCJZIdlrGmicBEcusby0q2KHDjTdBS76g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"154\" \/><\/p>\n<h2><span style=\"font-size: 17px;\"><strong>4.4 \u751f\u6210\u4e00\u4e2aSummarizedExperiment \u5bf9\u8c61<\/strong><\/span><\/h2>\n<h2 style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u8bb8\u591aBioconductor\u4f7f\u7528 SummarizedLaboratory \u5bf9\u8c61\u4f5c\u4e3a\u8f93\u5165\u548c\/\u6216\u8f93\u51fa\u3002\u8fd9\u7c7b\u5bf9\u8c61\u5305\u542b\u5e76\u534f\u8c03\u5b9e\u9645(\u5316\u9a8c)\u6570\u636e\u3001\u5173\u4e8e\u6837\u54c1\u7684\u4fe1\u606f\u4ee5\u53ca\u7279\u5f81\u6ce8\u91ca\u3002\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528\u4e24\u79cd\u4e0d\u540c\u7684\u65b9\u6cd5\u4ece\u6570\u636e\u4e2d\u751f\u6210 SummarizedLaboratory \u5bf9\u8c61\u3002\u6211\u4eec\u53ef\u4ee5\u76f4\u63a5\u4ece\u5217\u540d\u4e2d\u63d0\u53d6\u6837\u672c\u4fe1\u606f\uff0c\u6216\u8005\u4f7f\u7528\u5b9e\u9a8c\u8bbe\u8ba1\u6a21\u677f\u6dfb\u52a0\u6837\u672c\u4fe1\u606f\u3002\u793a\u4f8b\u6570\u636e\u96c6\u7684\u5305\u4e2d\u5305\u542b\u4e86\u4e00\u4e2a\u5b9e\u9a8c\u6027\u8bbe\u8ba1\u3002<\/span><\/h2>\n<h2 style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u5b9e\u9a8c\u8bbe\u8ba1\u5fc5\u987b\u5305\u542b\u201clabel\u201d\u3001\u201ccondition\u201d\u548c\u201creplicate\u201d\u5217\u3002\u201c\u6807\u7b7e\u201d\u5217\u5305\u542b\u4e0d\u540c\u6837\u54c1\u7684\u6807\u8bc6\u7b26\uff0c\u5b83\u4eec\u5e94\u8be5\u4e0e\u5305\u542b\u5316\u9a8c\u6570\u636e\u7684\u5217\u540d\u76f8\u5bf9\u5e94\u3002\u201c\u6761\u4ef6\u201d\u548c\u201c\u590d\u5236\u201d\u5217\u5305\u542b\u7528\u6237\u5b9a\u4e49\u7684\u8fd9\u4e9b\u793a\u4f8b\u7684\u6ce8\u91ca\u3002<\/span><\/h2>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"perl\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u6839\u636e\u5b9e\u9a8c\u8bbe\u8ba1\u751f\u6210\u4e00\u4e2aSummarizedExperiment\u5bf9\u8c61\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">LFQ_columns <- <span class=\"code-snippet__keyword\">grep<\/span>(<span class=\"code-snippet__string\">\"LFQ.\"<\/span>, colnames(data_unique))<\/span><\/code><code><span class=\"code-snippet_outer\">experimental_design <- UbiLength_ExpDesign<\/span><\/code><code><span class=\"code-snippet_outer\">data_se <- make_se(data_unique, LFQ_columns, experimental_design)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">LFQ_columns <- <span class=\"code-snippet__keyword\">grep<\/span>(<span class=\"code-snippet__string\">\"LFQ.\"<\/span>, colnames(data_unique)) <span class=\"code-snippet__comment\"># get LFQ column numbers<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">data_se_parsed <- make_se_parse(data_unique, LFQ_columns)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u73b0\u5728\u8ba9\u6211\u4eec\u770b\u4e00\u4e0b\u751f\u6210\u7684 SummarizedExperiment \u5bf9\u8c61<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">data_se<\/span><\/code><\/pre>\n<\/section>\n<h2><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.28964059196617337\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/5_BEnO3tt0Yb6oNicdUCz4VAJ8hnGYJg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZXGOfWhzkD8ia0YWxZqicefHfBbHBEnO3tt0Yb6oNicdUCz4VAJ8hnGYJg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"946\" \/><\/h2>\n<p><strong><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\">4.5 SummarizedExperiment\u7684\u5148\u51b3\u6761\u4ef6<\/span><\/strong><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/span><br \/><\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">Make _ se \u548c make _ se _ parse \u51fd\u6570\u751f\u6210\u4e00\u4e2a SummarizedLaboratory \u5bf9\u8c61\uff0c\u8be5\u5bf9\u8c61\u5177\u6709\u4e24\u4e2a\u89c4\u8303\u3002\u6d4b\u5b9a\u6570\u636e\u662f log2\u8f6c\u6362\u7684\uff0c\u5176\u884c\u540d\u63cf\u8ff0\u86cb\u767d\u8d28\u540d\u79f0\u3002RowData \u5305\u542b make _ only \u751f\u6210\u7684\u201c name\u201d\u548c\u201c ID\u201d\u5217\u3002ColData \u5305\u542b\u5b9e\u9a8c\u8bbe\u8ba1\uff0c\u4ece\u800c\u5305\u542b\u793a\u4f8b\u6ce8\u91ca\u3002\u56e0\u6b64\uff0ccolData \u5305\u62ec\u201c label\u201d\u3001\u201ccondition\u201d\u548c\u201creplicate\u201d\u5217\u4ee5\u53ca\u4e00\u4e2a\u65b0\u751f\u6210\u7684\u201c ID\u201d\u5217\u3002Log2\u8f6c\u6362\u7684\u6d4b\u5b9a\u6570\u636e\u548c\u6307\u5b9a\u7684 rowData \u548c colData \u5217\u662f\u540e\u7eed\u5206\u6790\u6b65\u9aa4\u7684\u5148\u51b3\u6761\u4ef6\u3002<\/span><\/p>\n<p><strong><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\">4.6 \u5bf9\u7f3a\u5931\u503c\u8fdb\u884c\u7b5b\u9009<\/span><\/strong><\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u6570\u636e\u96c6\u5305\u542b\u7684\u86cb\u767d\u8d28\u5e76\u975e\u5728\u6240\u6709\u91cd\u590d\u4e2d\u90fd\u88ab\u91cf\u5316\u3002\u6709\u4e9b\u86cb\u767d\u8d28\u751a\u81f3\u53ea\u5728\u4e00\u6b21\u91cd\u590d\u4e2d\u88ab\u91cf\u5316\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"apache\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236\u6837\u54c1\u95f4\u86cb\u767d\u8d28\u9274\u5b9a\u91cd\u53e0\u7684\u6761\u5f62\u56fe\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">plot_frequency<\/span>(data_se)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/6_gvxNRpI3tnY7C9SMYDImiaVJQ6xEHA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZpBP1UYKh1ibf0Wl7SSlsUWCFh5gvxNRpI3tnY7C9SMYDImiaVJQ6xEHA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" \/><\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u8fd9\u4f7f\u5f97\u6211\u4eec\u7684\u6570\u636e\u96c6\u5305\u542b\u5f88\u591a\u9700\u8981\u88ab\u586b\u5145\u7684\u7f3a\u5931\u503c\u3002\u7136\u800c\uff0c\u5bf9\u4e8e\u542b\u6709\u592a\u591a\u7f3a\u5931\u503c\u7684\u86cb\u767d\u8d28\u4e0d\u5e94\u8be5\u8fd9\u6837\u505a\u3002\u56e0\u6b64\uff0c\u6211\u4eec\u9996\u5148\u7b5b\u9009\u51fa\u542b\u6709\u592a\u591a\u7f3a\u5931\u503c\u7684\u86cb\u767d\u8d28\u3002\u8fd9\u662f\u901a\u8fc7\u5728 filter _ missval \u51fd\u6570\u4e2d\u4e3a\u6bcf\u4e2a\u6761\u4ef6\u5141\u8bb8\u7684\u7f3a\u5931\u503c\u6570\u91cf\u8bbe\u7f6e\u9608\u503c\u6765\u5b8c\u6210\u7684\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"properties\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u8fc7\u6ee4\u51fa\u6765\u81f3\u5c11\u5728\u4e00\u4e2a\u6761\u4ef6\u7684\u6240\u6709\u91cd\u590d\u4e2d\u88ab\u9274\u5b9a\u7684\u86cb\u767d\u8d28<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attr\">data_filt<\/span> <span class=\"code-snippet__string\"><- filter_missval(data_se, thr = 0)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attr\">data_filt2<\/span> <span class=\"code-snippet__string\"><- filter_missval(data_se, thr = 1)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236\u6bcf\u4e2a\u6837\u54c1\u4e2d\u9274\u5b9a\u51fa\u7684\u86cb\u767d\u8d28\u6570\u91cf\u7684\u6761\u5f62\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attr\">plot_numbers(data_filt)<\/span><\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/7_mFy3nYuWvLkv9mNE0KAGGCZ0oXHarA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZtooD43tzMFxR0zDa9zV58M9rmFy3nYuWvLkv9mNE0KAGGCZ0oXHarA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" \/><\/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=\"apache\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236\u6837\u54c1\u95f4\u86cb\u767d\u8d28\u9274\u5b9a\u91cd\u53e0\u7684\u6761\u5f62\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">plot_coverage<\/span>(data_filt)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/8_c7A1MtfibvoceiaZ9A9TOicgefZ5Cw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZmGdLyoRcQEHFPKPzDJK2kfYPTibTic7A1MtfibvoceiaZ9A9TOicgefZ5Cw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" \/><\/p>\n<p><strong><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\">4.7 \u5f52\u4e00\u5316<\/span><\/strong><br \/><\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u901a\u8fc7\u65b9\u5dee\u7a33\u5b9a\u5316\u53d8\u6362(vsn)\u5bf9\u6570\u636e\u8fdb\u884c\u80cc\u666f\u6821\u6b63\u548c\u5f52\u4e00\u5316\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u5f52\u4e00\u5316\u6570\u636e\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">data_norm<\/span> <- normalize_vsn(data_filt)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u901a\u8fc7\u7bb1\u5f62\u56fe\u5c55\u793a\u6240\u6709\u6837\u54c1\u5728\u5f52\u4e00\u5316\u524d\u540e\u7684\u533a\u522b\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">plot_normalization(data_filt, data_norm)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_jCHN5Nyct4NrExLzib1BNnm8mKnMsQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZzMRGE69cicibGZyP7W6mPaFlGzFjCHN5Nyct4NrExLzib1BNnm8mKnMsQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" data-recalc-dims=\"1\" \/><strong>4.8 <span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\">\u586b\u5145\u7f3a\u5931\u503c<\/span><\/strong><\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u9700\u8981\u4f30\u7b97\u6570\u636e\u96c6\u4e2d\u5176\u4f59\u7f3a\u5c11\u7684\u503c\u3002\u6570\u636e\u53ef\u80fd\u968f\u673a\u4e22\u5931(MAR) \uff0c\u4f8b\u5982\uff0c\u5982\u679c\u86cb\u767d\u8d28\u5728\u67d0\u4e9b\u91cd\u590d\u4e2d\u88ab\u91cf\u5316\uff0c\u800c\u5728\u5176\u4ed6\u91cd\u590d\u4e2d\u4e0d\u88ab\u91cf\u5316\u3002\u6570\u636e\u4e5f\u53ef\u80fd\u4e0d\u662f\u968f\u673a\u4e22\u5931(MNAR) \uff0c\u4f8b\u5982\uff0c\u5982\u679c\u86cb\u767d\u8d28\u6ca1\u6709\u5728\u7279\u5b9a\u6761\u4ef6\u4e0b\u5b9a\u91cf(\u4f8b\u5982\u5728\u5bf9\u7167\u6837\u54c1\u4e2d)\u3002MNAR \u53ef\u4ee5\u8868\u660e\u86cb\u767d\u8d28\u5728\u7279\u5b9a\u6837\u54c1\u4e2d\u4f4e\u4e8e\u68c0\u6d4b\u9650\uff0c\u8fd9\u5728\u86cb\u767d\u8d28\u7ec4\u5b66\u5b9e\u9a8c\u4e2d\u53ef\u80fd\u662f\u975e\u5e38\u597d\u7684\u60c5\u51b5\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"apache\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236\u5305\u542b\u7f3a\u5931\u503c\u7684\u86cb\u767d\u8d28\u70ed\u56fe\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">plot_missval<\/span>(data_filt)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/10_hpgdGjUlrCUrSYFR4UTGOJOl0F99Ig.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZCdbQ5wUciaPEslibSzgy1FdxWehpgdGjUlrCUrSYFR4UTGOJOl0F99Ig\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" \/><\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u8fd9\u4e2a\u70ed\u56fe\u8868\u660e\uff0c\u7f3a\u5931\u7684\u503c\u9ad8\u5ea6\u504f\u5411\u4e8e\u7279\u5b9a\u7684\u6837\u672c\u3002\u793a\u4f8b\u6570\u636e\u96c6\u662f\u6cdb\u7d20\u76f8\u4e92\u4f5c\u7528\u7684\u4eb2\u548c\u529b\u5bcc\u96c6\u6570\u636e\u96c6\uff0c\u5b83\u53ef\u80fd\u5728\u7279\u5b9a\u6837\u54c1\u4e2d\u5177\u6709\u4f4e\u4e8e\u68c0\u6d4b\u9650\u7684\u86cb\u767d\u8d28\u3002\u8fd9\u4e9b\u53ef\u80fd\u662f\u5728\u6cdb\u7d20\u7eaf\u5316\u4e2d\u7279\u5f02\u6027\u5bcc\u96c6\u7684\u86cb\u767d\u8d28\uff0c\u4f46\u5728\u5bf9\u7167\u6837\u54c1\u4e2d\u4e0d\u5bcc\u96c6\uff0c\u53cd\u4e4b\u4ea6\u7136\u3002\u4e3a\u4e86\u68c0\u67e5\u7f3a\u5931\u503c\u662f\u5426\u504f\u5411\u4e8e\u8f83\u4f4e\u5f3a\u5ea6\u7684\u86cb\u767d\u8d28\uff0c\u5bc6\u5ea6\u548c\u7d2f\u79ef\u5206\u6570\u7ed8\u5236\u4e86\u6709\u6216\u6ca1\u6709\u7f3a\u5931\u503c\u7684\u86cb\u767d\u8d28\u3002<\/span><br \/><\/p>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_joB3eJlBDh1rclXwPRFacS4jFOicZw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZiauHJpoucwxyicL89xibCFCHb9CSjoB3eJlBDh1rclXwPRFacS4jFOicZw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" data-recalc-dims=\"1\" \/><\/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=\"kotlin\"><code><span class=\"code-snippet_outer\"># \u4f7f\u7528\u4ee5\u6700\u5c0f\u503c\u4e3a\u4e2d\u5fc3\u7684\u968f\u673a\u62bd\u53d6\u7684\u6b63\u6001\u5206\u5e03\u586b\u5145\u7f3a\u5931\u7684\u6570\u636e\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">data_imp <- impute(data_norm, <span class=\"code-snippet__function\"><span class=\"code-snippet__keyword\">fun<\/span> = \"MinProb\", q = 0.01)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"># \u586b\u5145\u524d\u540e\u7684\u5f3a\u5ea6\u5206\u5e03\u56fe<\/span><\/code><code><span class=\"code-snippet_outer\">plot_imputation(data_norm, data_imp)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/12_SfeIdWSaJDrQdGEXLxpsb3hQtGCIsw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZa9ib6yGS6luZZoWUE0e2NjbEcSfeIdWSaJDrQdGEXLxpsb3hQtGCIsw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" \/><strong><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\">4.9 <\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\">\u5dee\u5f02\u5bcc\u96c6\u5206\u6790<\/span><\/strong><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"bash\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u57fa\u4e8e\u7ebf\u6027\u6a21\u578b\u548c\u8d1d\u53f6\u65af\u7edf\u8ba1\u7684\u5bcc\u96c6\u5206\u6790\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">data_diff <- test_diff(data_imp, <span class=\"code-snippet__built_in\">type<\/span> = <span class=\"code-snippet__string\">\"control\"<\/span>, control = <span class=\"code-snippet__string\">\"Ctrl\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">data_diff_all_contrasts <- test_diff(data_imp, <span class=\"code-snippet__built_in\">type<\/span> = <span class=\"code-snippet__string\">\"all\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">data_diff_manual <- test_diff(data_imp, <span class=\"code-snippet__built_in\">type<\/span> = <span class=\"code-snippet__string\">\"manual\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">test<\/span> = c(<span class=\"code-snippet__string\">\"Ubi4_vs_Ctrl\"<\/span>, <span class=\"code-snippet__string\">\"Ubi6_vs_Ctrl\"<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">dep <- add_rejections(data_diff, alpha = 0.05, lfc = log2(1.5))<\/span><\/code><\/pre>\n<\/section>\n<p><strong><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\">4.10 \u7ed3\u679c\u7684\u53ef\u89c6\u5316<\/span><\/strong><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/span><br \/><\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u524d\u9762\u5206\u6790\u7684\u7ed3\u679c\u53ef\u4ee5\u901a\u8fc7\u8bb8\u591a\u51fd\u6570\u5f88\u5bb9\u6613\u5730\u663e\u793a\u51fa\u6765\u3002\u8fd9\u4e9b\u53ef\u89c6\u5316\u6709\u52a9\u4e8e\u786e\u5b9a\u4f7f\u7528\u7684\u6700\u4f73cutoff\u503c\uff0c\u7a81\u51fa\u6700\u6709\u8da3\u7684\u6837\u54c1\u548c\u5bf9\u6bd4\u5ea6\uff0c\u5e76\u7cbe\u786e\u5b9a\u4f4d\u5dee\u5f02\u5bcc\u96c6\/\u8868\u8fbe\u7684\u86cb\u767d\u8d28\u3002<\/span><\/p>\n<p>4.10.1 PCA.<\/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=\"apache\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236\u7b2c\u4e00\u548c\u7b2c\u4e8c\u4e3b\u6210\u5206\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">plot_pca<\/span>(dep, x = 1, y = 2, n = 500, point_size = 4)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-croporisrc=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/13_Fs2ibWqX29cYXE4heTeATPH5ZcQvpQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZSI0jDLllia0b4WLrawpYP1xzkXFs2ibWqX29cYXE4heTeATPH5ZcQvpQ\/640?wx_fmt=png'\" data-cropx1=\"0\" data-cropx2=\"1080\" data-cropy1=\"0\" data-cropy2=\"723.114186851211\" data-ratio=\"0.6694444444444444\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/14_yplLJVloOTOJCIQL4Oj0NF5ic8icjw.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZFt2w9QicD85g6dQAFn2Ssicw7IcWyplLJVloOTOJCIQL4Oj0NF5ic8icjw\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"width: 578px;height: 387px;\" data-recalc-dims=\"1\" \/><\/p>\n<p>4.10.2 \u76f8\u5173\u6027\u7cfb\u6570\u77e9\u9635<\/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=\"objectivec\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\"># \u7ed8\u5236\u76f8\u5173\u7cfb\u6570\u77e9\u9635\u70ed\u56fe\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">plot_cor(dep, significant = <span class=\"code-snippet__literal\">TRUE<\/span>, lower = <span class=\"code-snippet__number\">0<\/span>, upper = <span class=\"code-snippet__number\">1<\/span>, pal = <span class=\"code-snippet__string\">\"Reds\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/15_BibkWI0CMrPPJrBx9OFxrNqicPlwlA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZ7TN2vwxRFbhkqVkibdbszeceF4zBibkWI0CMrPPJrBx9OFxrNqicPlwlA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" data-recalc-dims=\"1\" \/><\/p>\n<p>4.10.3 \u6240\u6709\u91cd\u8981\u86cb\u767d\u8d28\u7684\u70ed\u56fe<\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u70ed\u56fe\u8868\u793a\u7ed9\u51fa\u4e86\u6240\u6709\u6837\u54c1(\u5217)\u4e2d\u6240\u6709\u91cd\u8981\u86cb\u767d\u8d28(\u884c)\u7684\u6982\u8ff0\u3002\u8fd9\u6837\u53ef\u4ee5\u770b\u5230\u4e00\u822c\u8d8b\u52bf\uff0c\u4f8b\u5982\u4e00\u4e2a\u6837\u672c\u6216\u590d\u5236\u662f\u5426\u4e0e\u5176\u4ed6\u6837\u672c\u771f\u7684\u4e0d\u540c\u3002\u6b64\u5916\uff0c\u6837\u54c1(\u5217)\u7684\u805a\u7c7b\u53ef\u4ee5\u8868\u660e\u66f4\u5bc6\u5207\u7684\u76f8\u5173\u6837\u54c1\u548c\u86cb\u767d\u8d28(\u884c)\u7684\u805a\u7c7b\u8868\u660e\u7c7b\u4f3c\u7684\u884c\u4e3a\u86cb\u767d\u8d28\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"makefile\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236\u6240\u6709\u91cd\u8981\u86cb\u767d\u8d28\u7684\u70ed\u56fe\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">plot_heatmap(dep, type = <span class=\"code-snippet__string\">\"centered\"<\/span>, kmeans = TRUE,<\/span><\/code><code><span class=\"code-snippet_outer\">k = 6, col_limit = 4, show_row_names = FALSE,<\/span><\/code><code><span class=\"code-snippet_outer\">indicate = c(<span class=\"code-snippet__string\">\"condition\"<\/span>, <span class=\"code-snippet__string\">\"replicate\"<\/span>))<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/16_gUS8rrN83shuFCOuK4AgQWB1vXCTqw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZDVoXhicEf3qLokyFadbyBXNLEgUS8rrN83shuFCOuK4AgQWB1vXCTqw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" \/><\/p>\n<p>4.10.4 \u7ed8\u5236\u5dee\u5f02\u86cb\u767d\u706b\u5c71\u56fe<\/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=\"php\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236 \"Ubi6 vs Ctrl\"\"\u7684\u706b\u5c71\u56fe\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">plot_volcano(dep, contrast = <span class=\"code-snippet__string\">\"Ubi6_vs_Ctrl\"<\/span>, label_size = <span class=\"code-snippet__number\">2<\/span>, add_names = <span class=\"code-snippet__keyword\">TRUE<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/17_1a2MgkMibtaRZpnDfth8UTWzwByjqw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZsSmXYib7wX1ibz4icApDWRlZm2TQ1a2MgkMibtaRZpnDfth8UTWzwByjqw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" \/><\/p>\n<p>4.10.5 \u611f\u5174\u8da3\u86cb\u767d\u8d28\u7684\u6761\u5f62\u56fe<\/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=\"apache\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236 USP15 \u548c IKBKG \u7684\u6761\u5f62\u56fe\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">plot_single<\/span>(dep, proteins = c(<span class=\"code-snippet__string\">\"USP15\"<\/span>, <span class=\"code-snippet__string\">\"IKBKG\"<\/span>))<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/18_zpYB66d4z3ymrich1YfaGNXic2wzkQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZR5kldxPhb7kMJ3Oicic80F6nQREWzpYB66d4z3ymrich1YfaGNXic2wzkQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" data-recalc-dims=\"1\" \/><\/p>\n<p>4.10.6 \u91cd\u8981\u86cb\u767d\u7684\u9891\u7387\u56fe<\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\"># \u7ed8\u5236\u4e0d\u540c\u6761\u4ef6\u4e0b\u91cd\u8981\u86cb\u767d\u7684\u9891\u7387\u56fe<\/span><\/p>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/19_cHiaRHObG7pNibZsR6zxTKdf99rJxw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZoKF6MDZN6QdoSicW3trFEYu0hiaycHiaRHObG7pNibZsR6zxTKdf99rJxw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" \/><\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><strong><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u597d\u5566\uff0c\u4ee5\u4e0a\u5c31\u662f\u86cb\u767d\u8d28\u7ec4\u4e0b\u6e38\u5206\u6790\u8f6f\u4ef6\u5305DEP\u7684\u4f7f\u7528\u6559\u7a0b\uff0c\u5305\u62ec\u4e0b\u6e38\u6570\u636e\u5904\u7406\u4ee5\u53ca\u5dee\u5f02\u5bcc\u96c6\u5206\u6790\u7b49\uff0c\u5e0c\u671b\u5c0f\u679c\u53ef\u4ee5\u5e2e\u52a9\u5230\u4f60\uff01<\/span><\/strong><span style=\"letter-spacing: 0.034em;font-size: 14px;\"><\/span><\/p>\n<section powered-by=\"xiumi.us\" style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;text-align: left;\">\n<section style=\"font-size: 16px;\">\n<section powered-by=\"xiumi.us\" style=\"margin: 10px;justify-content: flex-start;display: flex;flex-flow: row;\">\n<section style=\"padding-right: 10px;padding-left: 10px;display: inline-block;width: 558px;vertical-align: top;border-style: dashed;border-width: 1px;border-color: rgb(62, 62, 62);align-self: flex-start;flex: 0 0 auto;\">\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 10px;\">\n<section style=\"display: inline-block;width: 536px;border-width: 0px 0px 0px 10px;border-style: solid;border-left-color: rgb(144, 215, 236);border-right-color: rgb(46, 172, 109);box-shadow: rgb(0, 0, 0) 0px 0px 0px;border-bottom-left-radius: 0px;\">\n<section powered-by=\"xiumi.us\" style=\"padding-right: 3px;padding-left: 3px;\">\n<section style=\"margin-top: 0.95em;margin-bottom: -0.65em;display: inline-block;width: 520px;vertical-align: top;\">\n<section style=\"margin-top: -1em;padding: 3px 10px;display: inline-block;vertical-align: top;background-color: rgb(255, 255, 255);color: rgb(0, 154, 68);\">\n<p><strong>\u5f80\u671f\u63a8\u8350<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"text-align: justify;\">\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491794&idx=1&sn=2b7a4de95169c79202e44813885a8250&chksm=cf7f7017f808f9015689839fe4057fd418bf7b20eb1dfb5a28cd92e56a41b5605e62bfbc16fb&scene=21#wechat_redirect\" textvalue=\"1.\u642d\u5efa\u751f\u4fe1\u5206\u6790\u6d41\u6c34\u7ebf\uff0c\u5982\u5de5\u5382\u4e00\u683724\u5c0f\u65f6\u8fd0\u8f6cSnakemake\u2014\u2014\u8fdb\u9636\u547d\u4ee4\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" 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0;align-items:center}.flex_bd{padding-left:14px;}.account_nickname{display:inline-block;vertical-align:middle;line-height:1.2;color:#576b95;font-size:14px}.account_desc{overflow:hidden;text-overflow:ellipsis;display:-webkit-box;-webkit-box-orient:vertical;-webkit-line-clamp:1;color:rgba(0,0,0,0.3);font-size:14px;line-height:1.2;padding-top:.4em}.msg_source_url{text-align:left;word-break:break-all;margin-top:20px;}.msg_source_url a{padding-right:10px;}.msg_source_url .url_text{color:#a8a8a8;}.video-desc{font-size:14px;margin-top:15px;color:#6c6c6c;}.msg_source_url{text-align:left;}.original_primary_card_tips{color:rgba(0,0,0,0.3);line-height:1.4;font-size:15px;}.weui-flex__item{margin-bottom:20px;padding:20px 16px;margin-top:16px;line-height:1.4;align-items:center;background-color:#f7f7f7;border-radius:8px;position:relative;}.original_primary_desc{color:rgba(0,0,0,0.5);font-size:14px;padding-top:4px;width:auto;overflow:hidden;text-overflow:ellipsis;}.msgBodyReplyList{border-top:1px 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data={\"mp\":\"\u751f\u4fe1\u679c\",\"title\":\"\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\",\"time\":\"2023-10-26 19:00:10\",\"timeStamp\":\"1698318010\"};\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=2247494801&idx=1&sn=03a9af53d1e11082d8d350e8f27e143d&chksm=cf7f7c54f808f54254a23d2582dd333047e2f4e1cfa222c717944c18b278f6be27349bc72adc#rd\" target=\"_blank\" rel=\"noopener\">\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01<\/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\">2023-10-26 19:00:10<\/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=2812010014583390210#wechat_redirect\" title=\"R\u4ee3\u7801\" target=\"_blank\" rel=\"noopener\">#R\u4ee3\u7801<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2664545260517294084#wechat_redirect\" title=\"\u751f\u4fe1\u5b9e\u64cd\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5b9e\u64cd<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2821072943068839938#wechat_redirect\" title=\"\u751f\u4fe1\u7ed8\u56fe\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u7ed8\u56fe<\/a><\/p>\n<\/div>\n<p data-mpa-powered-by=\"yiban.io\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u8fd1\u5e74\u6765\u968f\u7740\u8d28\u8c31\u4eea\u5668\u7684\u53d1\u5c55\uff0c\u86cb\u767d\u8d28\u7ec4\u5b66\u53d6\u5f97\u4e86\u957f\u8db3\u8fdb\u6b65\uff0c\u5728\u86cb\u767d\u8d28\u7ec4\u5b66\u6108\u52a0\u706b\u70ed\u7684\u4eca\u5929\uff0c\u8fd8\u4e0d\u8d76\u7d27\u5b66\u4e60\u86cb\u767d\u8d28\u7ec4\u7684\u5206\u6790\u65b9\u6cd5\uff1f\u597d\u7684\uff0c\u4eca\u5929\u5c31\u8ba9\u5c0f\u679c\u624b\u628a\u624b\u6559\u4f60\u5982\u4f55\u4f7f\u7528\u86cb\u767d\u8d28\u7ec4\u5206\u6790\u8f6f\u4ef6\u5305DEP\u5427\uff01<\/span><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">1.\u5206\u6790\u6982\u8ff0<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u8f6f\u4ef6\u5305DEP\u63d0\u4f9b\u4e86\u4e00\u4e2a\u96c6\u6210\u7684\u5206\u6790\u5de5\u4f5c\u6d41\u7a0b\uff0c\u7528\u4e8e\u5bf9\u5dee\u5f02\u86cb\u767d\u8d28\u8868\u8fbe\u6216\u5dee\u5f02\u5bcc\u96c6\u7684\u8d28\u8c31\u6cd5\u86cb\u767d\u8d28\u7ec4\u5b66\u6570\u636e\u8fdb\u884c\u53ef\u9760\u548c\u53ef\u91cd\u590d\u7684\u5206\u6790\u3002<\/span><span style=\"text-align: center;font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/span><\/p>\n<p style=\"text-align: left;\"><span style=\"font-size: 14px;letter-spacing: 0.034em;text-align: justify;\"><em style=\"letter-spacing: 0.578px;white-space: normal;color: rgb(178, 178, 178);\"><span style=\"font-size: 13px;text-decoration: underline;\">\u516c\u4f17\u53f7\u540e\u53f0\u56de\u590d\u201c111″,\u9886\u53d6\u4ee3\u7801\uff0c\u4ee3\u7801\u7f16\u53f7\uff1a231011<\/span><\/em><\/span><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">2.\u5b89\u88c5\u4ee5\u53ca\u52a0\u8f7dR\u5305<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">if<\/span> (!requireNamespace(<span class=\"code-snippet__string\">\"BiocManager\"<\/span>, quietly=<span class=\"code-snippet__keyword\">TRUE<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"BiocManager\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">BiocManager::install(<span class=\"code-snippet__string\">\"DEP\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">library(<span class=\"code-snippet__string\">\"DEP\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">3.\u4ea4\u4e92\u5f0f\u4f7f\u7528\uff08\u53ef\u9009\uff09<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u8be5\u8f6f\u4ef6\u5305\u5305\u542bshiny\u7684\u5e94\u7528\u7a0b\u5e8f\uff0c\u5b83\u5141\u8bb8\u4e0b\u9762\u63cf\u8ff0\u7684\u6574\u4e2a\u5de5\u4f5c\u6d41\u7a0b\u7684\u4ea4\u4e92\u5f0f\u5206\u6790\u3002\u8fd9\u4e9b\u5e94\u7528\u7a0b\u5e8f\u7279\u522b\u9002\u7528\u4e8e\u6709\u9650\u6216\u6ca1\u6709 R \u7ecf\u9a8c\u7684\u7528\u6237\u3002\u76ee\u524d\uff0c\u6709\u4e24\u79cd\u4e0d\u540c\u7684\u5e94\u7528\u7a0b\u5e8f\u3002\u4e00\u4e2a\u7528\u4e8e\u57fa\u4e8e\u65e0\u6807\u7b7e\u5b9a\u91cf(LFQ)\u7684\u5206\u6790(\u6765\u81ea MaxQuant \u7684\u8f93\u51fa) \uff0c\u53e6\u4e00\u4e2a\u7528\u4e8e\u57fa\u4e8e\u4e32\u8054\u8d28\u91cf\u6807\u7b7e(TMT)\u7684\u5206\u6790(\u6765\u81ea IsobarQuant \u7684\u8f93\u51fa)\u3002\u8981\u8fd0\u884c\u8fd9\u4e9b\u5e94\u7528\u7a0b\u5e8f\uff0c\u53ea\u9700\u8fd0\u884c\u4ee5\u4e0b\u547d\u4ee4:<\/span><br \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"apache\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7528\u4e8e LFQ \u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">run_app<\/span>(<span class=\"code-snippet__string\">\"LFQ\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7528\u4e8e TMT \u5206\u6790<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">run_app<\/span>(<span class=\"code-snippet__string\">\"TMT\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">4.\u5dee\u5f02\u8868\u8fbe\u5206\u6790<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u6211\u4eec\u5206\u6790\u4e86\u6cdb\u7d20-\u86cb\u767d\u8d28\u76f8\u4e92\u4f5c\u7528\u7684\u86cb\u767d\u8d28\u7ec4\u5b66\u6570\u636e\u96c6(Zhang et al. Mol Cell 2017)\u3002\u539f\u59cb\u8d28\u8c31\u6570\u636e\u9996\u5148\u4f7f\u7528 MaxQuant (Cox and Mann, Nat Biotech 2007)\u8fdb\u884c\u5206\u6790\uff0c\u7ecf\u8fc7\u5206\u6790\u4e4b\u540e\u5f97\u5230\u7684\u201c proteininGroups.txt\u201d\u6587\u4ef6\u7528\u4f5c\u4e0b\u6e38\u5206\u6790\u7684\u8f93\u5165\u3002<\/span><\/p>\n<p><strong>4.1 \u6837\u54c1\u6570\u636e\u96c6<\/strong>\uff1a<span style=\"letter-spacing: 0.034em;font-size: 14px;\">Ubiquitin interactors<\/span><\/p>\n<p><strong>4.2 \u5bfc\u5165\u6570\u636e<\/strong><\/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<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<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=\"powershell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u5bfc\u5165\u7528\u4e8e\u6570\u636e\u5904\u7406\u7684\u8f6f\u4ef6\u5305\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(<span class=\"code-snippet__string\">\"dplyr\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u8fd9\u91cc\u6211\u4eec\u4f7f\u7528\u8f6f\u4ef6\u5305\u81ea\u5e26\u7684\u6570\u636e\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">data<\/span> <- UbiLength<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u6211\u4eec\u7b5b\u9009\u6c61\u67d3\u86cb\u767d\u8d28\u548c\u8bf1\u9975\u6570\u636e\u5e93\u5339\u914d\u7ed3\u679c\uff0c\u5b83\u4eec\u5206\u522b\u7531\u201cPotential.contaminants\u201d\u548c\u201cReverse\u201d\u5217\u4e2d\u7684\u201c +\u201d\u8868\u793a<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">data<\/span> <- <span class=\"code-snippet__keyword\">filter<\/span>(<span class=\"code-snippet__keyword\">data<\/span>, Reverse != <span class=\"code-snippet__string\">\"+\"<\/span>, Potential.contaminant != <span class=\"code-snippet__string\">\"+\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">The data.frame has the following dimensions:<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">dim(<span class=\"code-snippet__keyword\">data<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## [1] 2941 23<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">The data.frame has the following column names:<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">colnames(<span class=\"code-snippet__keyword\">data<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.15462962962962962\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/1_WMGDdw7aFnDURJdmibJaTDXOIBqrVw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZOia2vAdicnKibuEy40EbJljZGu1PWMGDdw7aFnDURJdmibJaTDXOIBqrVw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" \/><\/p>\n<p><strong>4.3\u6570\u636e\u51c6\u5907<\/strong><\/p>\n<p><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u6211\u4eec\u786e\u8ba4\u6570\u636e\u96c6\u662f\u5426\u5177\u6709\u552f\u4e00\u7684 Uniprot \u6807\u8bc6\u7b26<\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"powershell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u5148\u5224\u65ad\u6570\u636e\u96c6\u662f\u5426\u6709\u91cd\u590d\u7684\u57fa\u56e0\u540d?<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">data<\/span><span class=\"code-snippet__variable\">$Gene<\/span>.names %>% duplicated() %>% any()<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.09597523219814241\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/2_7fdiaDWw1la4NLzGD9LjQe64axjOMg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZbxlY7KfrO7Tko8SeYpCe5Ea9K7fdiaDWw1la4NLzGD9LjQe64axjOMg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"646\" \/><\/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=\"powershell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u5236\u4f5c\u4e00\u4e2a\u91cd\u590d\u57fa\u56e0\u540d\u79f0\u7684\u8868\u683c\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">data<\/span> %>% group_by(Gene.names) %>% summarize(frequency = n()) %>%<\/span><\/code><code><span class=\"code-snippet_outer\">arrange(desc(frequency)) %>% <span class=\"code-snippet__keyword\">filter<\/span>(frequency > <span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.8529411764705882\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/3_kEglJiaqibJnmsBPHAI12d54WpdpnQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZvuWVc3yPAaMSGKUP8GWpbNicgmakEglJiaqibJnmsBPHAI12d54WpdpnQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"612\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"powershell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u4e3a\u4e86\u8fdb\u4e00\u6b65\u5206\u6790\uff0c\u8fd9\u4e9b\u86cb\u767d\u8d28\u5fc5\u987b\u5f97\u5230\u552f\u4e00\u7684\u540d\u79f0\u3002\u6b64\u5916\uff0c\u4e00\u4e9b\u86cb\u767d\u8d28\u6ca1\u6709\u6ce8\u91ca\u7684\u57fa\u56e0\u540d\u79f0\uff0c\u5bf9\u4e8e\u8fd9\u4e9b\uff0c\u6211\u4eec\u5c06\u4f7f\u7528 Uniprot ID<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">data_unique <- make_unique(<span class=\"code-snippet__keyword\">data<\/span>, <span class=\"code-snippet__string\">\"Gene.names\"<\/span>, <span class=\"code-snippet__string\">\"Protein.IDs\"<\/span>, delim = <span class=\"code-snippet__string\">\";\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># Are there any duplicated names?<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">data<\/span><span class=\"code-snippet__variable\">$name<\/span> %>% duplicated() %>% any()<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.24675324675324675\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/4_ZIdlrGmicBEcusby0q2KHDjTdBS76g.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZzXXQKzT8WbZRHgWto4KxPiaNCJZIdlrGmicBEcusby0q2KHDjTdBS76g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"154\" \/><\/p>\n<h2><span style=\"font-size: 17px;\"><strong>4.4 \u751f\u6210\u4e00\u4e2aSummarizedExperiment \u5bf9\u8c61<\/strong><\/span><\/h2>\n<h2 style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u8bb8\u591aBioconductor\u4f7f\u7528 SummarizedLaboratory \u5bf9\u8c61\u4f5c\u4e3a\u8f93\u5165\u548c\/\u6216\u8f93\u51fa\u3002\u8fd9\u7c7b\u5bf9\u8c61\u5305\u542b\u5e76\u534f\u8c03\u5b9e\u9645(\u5316\u9a8c)\u6570\u636e\u3001\u5173\u4e8e\u6837\u54c1\u7684\u4fe1\u606f\u4ee5\u53ca\u7279\u5f81\u6ce8\u91ca\u3002\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528\u4e24\u79cd\u4e0d\u540c\u7684\u65b9\u6cd5\u4ece\u6570\u636e\u4e2d\u751f\u6210 SummarizedLaboratory \u5bf9\u8c61\u3002\u6211\u4eec\u53ef\u4ee5\u76f4\u63a5\u4ece\u5217\u540d\u4e2d\u63d0\u53d6\u6837\u672c\u4fe1\u606f\uff0c\u6216\u8005\u4f7f\u7528\u5b9e\u9a8c\u8bbe\u8ba1\u6a21\u677f\u6dfb\u52a0\u6837\u672c\u4fe1\u606f\u3002\u793a\u4f8b\u6570\u636e\u96c6\u7684\u5305\u4e2d\u5305\u542b\u4e86\u4e00\u4e2a\u5b9e\u9a8c\u6027\u8bbe\u8ba1\u3002<\/span><\/h2>\n<h2 style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u5b9e\u9a8c\u8bbe\u8ba1\u5fc5\u987b\u5305\u542b\u201clabel\u201d\u3001\u201ccondition\u201d\u548c\u201creplicate\u201d\u5217\u3002\u201c\u6807\u7b7e\u201d\u5217\u5305\u542b\u4e0d\u540c\u6837\u54c1\u7684\u6807\u8bc6\u7b26\uff0c\u5b83\u4eec\u5e94\u8be5\u4e0e\u5305\u542b\u5316\u9a8c\u6570\u636e\u7684\u5217\u540d\u76f8\u5bf9\u5e94\u3002\u201c\u6761\u4ef6\u201d\u548c\u201c\u590d\u5236\u201d\u5217\u5305\u542b\u7528\u6237\u5b9a\u4e49\u7684\u8fd9\u4e9b\u793a\u4f8b\u7684\u6ce8\u91ca\u3002<\/span><\/h2>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"perl\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u6839\u636e\u5b9e\u9a8c\u8bbe\u8ba1\u751f\u6210\u4e00\u4e2aSummarizedExperiment\u5bf9\u8c61\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">LFQ_columns <- <span class=\"code-snippet__keyword\">grep<\/span>(<span class=\"code-snippet__string\">\"LFQ.\"<\/span>, colnames(data_unique))<\/span><\/code><code><span class=\"code-snippet_outer\">experimental_design <- UbiLength_ExpDesign<\/span><\/code><code><span class=\"code-snippet_outer\">data_se <- make_se(data_unique, LFQ_columns, experimental_design)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">LFQ_columns <- <span class=\"code-snippet__keyword\">grep<\/span>(<span class=\"code-snippet__string\">\"LFQ.\"<\/span>, colnames(data_unique)) <span class=\"code-snippet__comment\"># get LFQ column numbers<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">data_se_parsed <- make_se_parse(data_unique, LFQ_columns)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u73b0\u5728\u8ba9\u6211\u4eec\u770b\u4e00\u4e0b\u751f\u6210\u7684 SummarizedExperiment \u5bf9\u8c61<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">data_se<\/span><\/code><\/pre>\n<\/section>\n<h2><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.28964059196617337\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/5_BEnO3tt0Yb6oNicdUCz4VAJ8hnGYJg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZXGOfWhzkD8ia0YWxZqicefHfBbHBEnO3tt0Yb6oNicdUCz4VAJ8hnGYJg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"946\" \/><\/h2>\n<p><strong><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\">4.5 SummarizedExperiment\u7684\u5148\u51b3\u6761\u4ef6<\/span><\/strong><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/span><br \/><\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">Make _ se \u548c make _ se _ parse \u51fd\u6570\u751f\u6210\u4e00\u4e2a SummarizedLaboratory \u5bf9\u8c61\uff0c\u8be5\u5bf9\u8c61\u5177\u6709\u4e24\u4e2a\u89c4\u8303\u3002\u6d4b\u5b9a\u6570\u636e\u662f log2\u8f6c\u6362\u7684\uff0c\u5176\u884c\u540d\u63cf\u8ff0\u86cb\u767d\u8d28\u540d\u79f0\u3002RowData \u5305\u542b make _ only \u751f\u6210\u7684\u201c name\u201d\u548c\u201c ID\u201d\u5217\u3002ColData \u5305\u542b\u5b9e\u9a8c\u8bbe\u8ba1\uff0c\u4ece\u800c\u5305\u542b\u793a\u4f8b\u6ce8\u91ca\u3002\u56e0\u6b64\uff0ccolData \u5305\u62ec\u201c label\u201d\u3001\u201ccondition\u201d\u548c\u201creplicate\u201d\u5217\u4ee5\u53ca\u4e00\u4e2a\u65b0\u751f\u6210\u7684\u201c ID\u201d\u5217\u3002Log2\u8f6c\u6362\u7684\u6d4b\u5b9a\u6570\u636e\u548c\u6307\u5b9a\u7684 rowData \u548c colData \u5217\u662f\u540e\u7eed\u5206\u6790\u6b65\u9aa4\u7684\u5148\u51b3\u6761\u4ef6\u3002<\/span><\/p>\n<p><strong><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\">4.6 \u5bf9\u7f3a\u5931\u503c\u8fdb\u884c\u7b5b\u9009<\/span><\/strong><\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u6570\u636e\u96c6\u5305\u542b\u7684\u86cb\u767d\u8d28\u5e76\u975e\u5728\u6240\u6709\u91cd\u590d\u4e2d\u90fd\u88ab\u91cf\u5316\u3002\u6709\u4e9b\u86cb\u767d\u8d28\u751a\u81f3\u53ea\u5728\u4e00\u6b21\u91cd\u590d\u4e2d\u88ab\u91cf\u5316\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"apache\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236\u6837\u54c1\u95f4\u86cb\u767d\u8d28\u9274\u5b9a\u91cd\u53e0\u7684\u6761\u5f62\u56fe\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">plot_frequency<\/span>(data_se)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/6_gvxNRpI3tnY7C9SMYDImiaVJQ6xEHA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZpBP1UYKh1ibf0Wl7SSlsUWCFh5gvxNRpI3tnY7C9SMYDImiaVJQ6xEHA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" \/><\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u8fd9\u4f7f\u5f97\u6211\u4eec\u7684\u6570\u636e\u96c6\u5305\u542b\u5f88\u591a\u9700\u8981\u88ab\u586b\u5145\u7684\u7f3a\u5931\u503c\u3002\u7136\u800c\uff0c\u5bf9\u4e8e\u542b\u6709\u592a\u591a\u7f3a\u5931\u503c\u7684\u86cb\u767d\u8d28\u4e0d\u5e94\u8be5\u8fd9\u6837\u505a\u3002\u56e0\u6b64\uff0c\u6211\u4eec\u9996\u5148\u7b5b\u9009\u51fa\u542b\u6709\u592a\u591a\u7f3a\u5931\u503c\u7684\u86cb\u767d\u8d28\u3002\u8fd9\u662f\u901a\u8fc7\u5728 filter _ missval \u51fd\u6570\u4e2d\u4e3a\u6bcf\u4e2a\u6761\u4ef6\u5141\u8bb8\u7684\u7f3a\u5931\u503c\u6570\u91cf\u8bbe\u7f6e\u9608\u503c\u6765\u5b8c\u6210\u7684\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"properties\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u8fc7\u6ee4\u51fa\u6765\u81f3\u5c11\u5728\u4e00\u4e2a\u6761\u4ef6\u7684\u6240\u6709\u91cd\u590d\u4e2d\u88ab\u9274\u5b9a\u7684\u86cb\u767d\u8d28<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attr\">data_filt<\/span> <span class=\"code-snippet__string\"><- filter_missval(data_se, thr = 0)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attr\">data_filt2<\/span> <span class=\"code-snippet__string\"><- filter_missval(data_se, thr = 1)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236\u6bcf\u4e2a\u6837\u54c1\u4e2d\u9274\u5b9a\u51fa\u7684\u86cb\u767d\u8d28\u6570\u91cf\u7684\u6761\u5f62\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attr\">plot_numbers(data_filt)<\/span><\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/7_mFy3nYuWvLkv9mNE0KAGGCZ0oXHarA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZtooD43tzMFxR0zDa9zV58M9rmFy3nYuWvLkv9mNE0KAGGCZ0oXHarA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" \/><\/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=\"apache\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236\u6837\u54c1\u95f4\u86cb\u767d\u8d28\u9274\u5b9a\u91cd\u53e0\u7684\u6761\u5f62\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">plot_coverage<\/span>(data_filt)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/8_c7A1MtfibvoceiaZ9A9TOicgefZ5Cw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZmGdLyoRcQEHFPKPzDJK2kfYPTibTic7A1MtfibvoceiaZ9A9TOicgefZ5Cw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" \/><\/p>\n<p><strong><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\">4.7 \u5f52\u4e00\u5316<\/span><\/strong><br \/><\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u901a\u8fc7\u65b9\u5dee\u7a33\u5b9a\u5316\u53d8\u6362(vsn)\u5bf9\u6570\u636e\u8fdb\u884c\u80cc\u666f\u6821\u6b63\u548c\u5f52\u4e00\u5316\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u5f52\u4e00\u5316\u6570\u636e\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">data_norm<\/span> <- normalize_vsn(data_filt)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u901a\u8fc7\u7bb1\u5f62\u56fe\u5c55\u793a\u6240\u6709\u6837\u54c1\u5728\u5f52\u4e00\u5316\u524d\u540e\u7684\u533a\u522b\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">plot_normalization(data_filt, data_norm)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_jCHN5Nyct4NrExLzib1BNnm8mKnMsQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZzMRGE69cicibGZyP7W6mPaFlGzFjCHN5Nyct4NrExLzib1BNnm8mKnMsQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" data-recalc-dims=\"1\" \/><strong>4.8 <span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\">\u586b\u5145\u7f3a\u5931\u503c<\/span><\/strong><\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u9700\u8981\u4f30\u7b97\u6570\u636e\u96c6\u4e2d\u5176\u4f59\u7f3a\u5c11\u7684\u503c\u3002\u6570\u636e\u53ef\u80fd\u968f\u673a\u4e22\u5931(MAR) \uff0c\u4f8b\u5982\uff0c\u5982\u679c\u86cb\u767d\u8d28\u5728\u67d0\u4e9b\u91cd\u590d\u4e2d\u88ab\u91cf\u5316\uff0c\u800c\u5728\u5176\u4ed6\u91cd\u590d\u4e2d\u4e0d\u88ab\u91cf\u5316\u3002\u6570\u636e\u4e5f\u53ef\u80fd\u4e0d\u662f\u968f\u673a\u4e22\u5931(MNAR) \uff0c\u4f8b\u5982\uff0c\u5982\u679c\u86cb\u767d\u8d28\u6ca1\u6709\u5728\u7279\u5b9a\u6761\u4ef6\u4e0b\u5b9a\u91cf(\u4f8b\u5982\u5728\u5bf9\u7167\u6837\u54c1\u4e2d)\u3002MNAR \u53ef\u4ee5\u8868\u660e\u86cb\u767d\u8d28\u5728\u7279\u5b9a\u6837\u54c1\u4e2d\u4f4e\u4e8e\u68c0\u6d4b\u9650\uff0c\u8fd9\u5728\u86cb\u767d\u8d28\u7ec4\u5b66\u5b9e\u9a8c\u4e2d\u53ef\u80fd\u662f\u975e\u5e38\u597d\u7684\u60c5\u51b5\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"apache\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236\u5305\u542b\u7f3a\u5931\u503c\u7684\u86cb\u767d\u8d28\u70ed\u56fe\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">plot_missval<\/span>(data_filt)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/10_hpgdGjUlrCUrSYFR4UTGOJOl0F99Ig.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZCdbQ5wUciaPEslibSzgy1FdxWehpgdGjUlrCUrSYFR4UTGOJOl0F99Ig\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" \/><\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u8fd9\u4e2a\u70ed\u56fe\u8868\u660e\uff0c\u7f3a\u5931\u7684\u503c\u9ad8\u5ea6\u504f\u5411\u4e8e\u7279\u5b9a\u7684\u6837\u672c\u3002\u793a\u4f8b\u6570\u636e\u96c6\u662f\u6cdb\u7d20\u76f8\u4e92\u4f5c\u7528\u7684\u4eb2\u548c\u529b\u5bcc\u96c6\u6570\u636e\u96c6\uff0c\u5b83\u53ef\u80fd\u5728\u7279\u5b9a\u6837\u54c1\u4e2d\u5177\u6709\u4f4e\u4e8e\u68c0\u6d4b\u9650\u7684\u86cb\u767d\u8d28\u3002\u8fd9\u4e9b\u53ef\u80fd\u662f\u5728\u6cdb\u7d20\u7eaf\u5316\u4e2d\u7279\u5f02\u6027\u5bcc\u96c6\u7684\u86cb\u767d\u8d28\uff0c\u4f46\u5728\u5bf9\u7167\u6837\u54c1\u4e2d\u4e0d\u5bcc\u96c6\uff0c\u53cd\u4e4b\u4ea6\u7136\u3002\u4e3a\u4e86\u68c0\u67e5\u7f3a\u5931\u503c\u662f\u5426\u504f\u5411\u4e8e\u8f83\u4f4e\u5f3a\u5ea6\u7684\u86cb\u767d\u8d28\uff0c\u5bc6\u5ea6\u548c\u7d2f\u79ef\u5206\u6570\u7ed8\u5236\u4e86\u6709\u6216\u6ca1\u6709\u7f3a\u5931\u503c\u7684\u86cb\u767d\u8d28\u3002<\/span><br \/><\/p>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_joB3eJlBDh1rclXwPRFacS4jFOicZw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZiauHJpoucwxyicL89xibCFCHb9CSjoB3eJlBDh1rclXwPRFacS4jFOicZw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" data-recalc-dims=\"1\" \/><\/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=\"kotlin\"><code><span class=\"code-snippet_outer\"># \u4f7f\u7528\u4ee5\u6700\u5c0f\u503c\u4e3a\u4e2d\u5fc3\u7684\u968f\u673a\u62bd\u53d6\u7684\u6b63\u6001\u5206\u5e03\u586b\u5145\u7f3a\u5931\u7684\u6570\u636e\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">data_imp <- impute(data_norm, <span class=\"code-snippet__function\"><span class=\"code-snippet__keyword\">fun<\/span> = \"MinProb\", q = 0.01)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"># \u586b\u5145\u524d\u540e\u7684\u5f3a\u5ea6\u5206\u5e03\u56fe<\/span><\/code><code><span class=\"code-snippet_outer\">plot_imputation(data_norm, data_imp)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/12_SfeIdWSaJDrQdGEXLxpsb3hQtGCIsw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZa9ib6yGS6luZZoWUE0e2NjbEcSfeIdWSaJDrQdGEXLxpsb3hQtGCIsw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" \/><strong><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\">4.9 <\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\">\u5dee\u5f02\u5bcc\u96c6\u5206\u6790<\/span><\/strong><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"bash\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u57fa\u4e8e\u7ebf\u6027\u6a21\u578b\u548c\u8d1d\u53f6\u65af\u7edf\u8ba1\u7684\u5bcc\u96c6\u5206\u6790\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">data_diff <- test_diff(data_imp, <span class=\"code-snippet__built_in\">type<\/span> = <span class=\"code-snippet__string\">\"control\"<\/span>, control = <span class=\"code-snippet__string\">\"Ctrl\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">data_diff_all_contrasts <- test_diff(data_imp, <span class=\"code-snippet__built_in\">type<\/span> = <span class=\"code-snippet__string\">\"all\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">data_diff_manual <- test_diff(data_imp, <span class=\"code-snippet__built_in\">type<\/span> = <span class=\"code-snippet__string\">\"manual\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">test<\/span> = c(<span class=\"code-snippet__string\">\"Ubi4_vs_Ctrl\"<\/span>, <span class=\"code-snippet__string\">\"Ubi6_vs_Ctrl\"<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">dep <- add_rejections(data_diff, alpha = 0.05, lfc = log2(1.5))<\/span><\/code><\/pre>\n<\/section>\n<p><strong><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\">4.10 \u7ed3\u679c\u7684\u53ef\u89c6\u5316<\/span><\/strong><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\"><\/span><br \/><\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u524d\u9762\u5206\u6790\u7684\u7ed3\u679c\u53ef\u4ee5\u901a\u8fc7\u8bb8\u591a\u51fd\u6570\u5f88\u5bb9\u6613\u5730\u663e\u793a\u51fa\u6765\u3002\u8fd9\u4e9b\u53ef\u89c6\u5316\u6709\u52a9\u4e8e\u786e\u5b9a\u4f7f\u7528\u7684\u6700\u4f73cutoff\u503c\uff0c\u7a81\u51fa\u6700\u6709\u8da3\u7684\u6837\u54c1\u548c\u5bf9\u6bd4\u5ea6\uff0c\u5e76\u7cbe\u786e\u5b9a\u4f4d\u5dee\u5f02\u5bcc\u96c6\/\u8868\u8fbe\u7684\u86cb\u767d\u8d28\u3002<\/span><\/p>\n<p>4.10.1 PCA.<\/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=\"apache\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236\u7b2c\u4e00\u548c\u7b2c\u4e8c\u4e3b\u6210\u5206\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">plot_pca<\/span>(dep, x = 1, y = 2, n = 500, point_size = 4)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-croporisrc=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/13_Fs2ibWqX29cYXE4heTeATPH5ZcQvpQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZSI0jDLllia0b4WLrawpYP1xzkXFs2ibWqX29cYXE4heTeATPH5ZcQvpQ\/640?wx_fmt=png'\" data-cropx1=\"0\" data-cropx2=\"1080\" data-cropy1=\"0\" data-cropy2=\"723.114186851211\" data-ratio=\"0.6694444444444444\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/14_yplLJVloOTOJCIQL4Oj0NF5ic8icjw.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZFt2w9QicD85g6dQAFn2Ssicw7IcWyplLJVloOTOJCIQL4Oj0NF5ic8icjw\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"width: 578px;height: 387px;\" data-recalc-dims=\"1\" \/><\/p>\n<p>4.10.2 \u76f8\u5173\u6027\u7cfb\u6570\u77e9\u9635<\/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=\"objectivec\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\"># \u7ed8\u5236\u76f8\u5173\u7cfb\u6570\u77e9\u9635\u70ed\u56fe\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">plot_cor(dep, significant = <span class=\"code-snippet__literal\">TRUE<\/span>, lower = <span class=\"code-snippet__number\">0<\/span>, upper = <span class=\"code-snippet__number\">1<\/span>, pal = <span class=\"code-snippet__string\">\"Reds\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/15_BibkWI0CMrPPJrBx9OFxrNqicPlwlA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZ7TN2vwxRFbhkqVkibdbszeceF4zBibkWI0CMrPPJrBx9OFxrNqicPlwlA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" data-recalc-dims=\"1\" \/><\/p>\n<p>4.10.3 \u6240\u6709\u91cd\u8981\u86cb\u767d\u8d28\u7684\u70ed\u56fe<\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u70ed\u56fe\u8868\u793a\u7ed9\u51fa\u4e86\u6240\u6709\u6837\u54c1(\u5217)\u4e2d\u6240\u6709\u91cd\u8981\u86cb\u767d\u8d28(\u884c)\u7684\u6982\u8ff0\u3002\u8fd9\u6837\u53ef\u4ee5\u770b\u5230\u4e00\u822c\u8d8b\u52bf\uff0c\u4f8b\u5982\u4e00\u4e2a\u6837\u672c\u6216\u590d\u5236\u662f\u5426\u4e0e\u5176\u4ed6\u6837\u672c\u771f\u7684\u4e0d\u540c\u3002\u6b64\u5916\uff0c\u6837\u54c1(\u5217)\u7684\u805a\u7c7b\u53ef\u4ee5\u8868\u660e\u66f4\u5bc6\u5207\u7684\u76f8\u5173\u6837\u54c1\u548c\u86cb\u767d\u8d28(\u884c)\u7684\u805a\u7c7b\u8868\u660e\u7c7b\u4f3c\u7684\u884c\u4e3a\u86cb\u767d\u8d28\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"makefile\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236\u6240\u6709\u91cd\u8981\u86cb\u767d\u8d28\u7684\u70ed\u56fe\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">plot_heatmap(dep, type = <span class=\"code-snippet__string\">\"centered\"<\/span>, kmeans = TRUE,<\/span><\/code><code><span class=\"code-snippet_outer\">k = 6, col_limit = 4, show_row_names = FALSE,<\/span><\/code><code><span class=\"code-snippet_outer\">indicate = c(<span class=\"code-snippet__string\">\"condition\"<\/span>, <span class=\"code-snippet__string\">\"replicate\"<\/span>))<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/16_gUS8rrN83shuFCOuK4AgQWB1vXCTqw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZDVoXhicEf3qLokyFadbyBXNLEgUS8rrN83shuFCOuK4AgQWB1vXCTqw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" \/><\/p>\n<p>4.10.4 \u7ed8\u5236\u5dee\u5f02\u86cb\u767d\u706b\u5c71\u56fe<\/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=\"php\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236 \"Ubi6 vs Ctrl\"\"\u7684\u706b\u5c71\u56fe\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">plot_volcano(dep, contrast = <span class=\"code-snippet__string\">\"Ubi6_vs_Ctrl\"<\/span>, label_size = <span class=\"code-snippet__number\">2<\/span>, add_names = <span class=\"code-snippet__keyword\">TRUE<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/17_1a2MgkMibtaRZpnDfth8UTWzwByjqw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZsSmXYib7wX1ibz4icApDWRlZm2TQ1a2MgkMibtaRZpnDfth8UTWzwByjqw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" \/><\/p>\n<p>4.10.5 \u611f\u5174\u8da3\u86cb\u767d\u8d28\u7684\u6761\u5f62\u56fe<\/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=\"apache\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u7ed8\u5236 USP15 \u548c IKBKG \u7684\u6761\u5f62\u56fe\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">plot_single<\/span>(dep, proteins = c(<span class=\"code-snippet__string\">\"USP15\"<\/span>, <span class=\"code-snippet__string\">\"IKBKG\"<\/span>))<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/18_zpYB66d4z3ymrich1YfaGNXic2wzkQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZR5kldxPhb7kMJ3Oicic80F6nQREWzpYB66d4z3ymrich1YfaGNXic2wzkQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" data-recalc-dims=\"1\" \/><\/p>\n<p>4.10.6 \u91cd\u8981\u86cb\u767d\u7684\u9891\u7387\u56fe<\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><span style=\"letter-spacing: 0.034em;font-size: 14px;\"># \u7ed8\u5236\u4e0d\u540c\u6761\u4ef6\u4e0b\u91cd\u8981\u86cb\u767d\u7684\u9891\u7387\u56fe<\/span><\/p>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7824074074074074\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-26_\u505a\u86cb\u767d\u7ec4\u7684\u540c\u5b66\u770b\u8fc7\u6765\uff01DEP\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\/19_cHiaRHObG7pNibZsR6zxTKdf99rJxw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZoKF6MDZN6QdoSicW3trFEYu0hiaycHiaRHObG7pNibZsR6zxTKdf99rJxw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" \/><\/p>\n<p style=\"letter-spacing: 0.034em;font-size: 14px;\"><strong><span style=\"letter-spacing: 0.034em;font-size: 14px;\">\u597d\u5566\uff0c\u4ee5\u4e0a\u5c31\u662f\u86cb\u767d\u8d28\u7ec4\u4e0b\u6e38\u5206\u6790\u8f6f\u4ef6\u5305DEP\u7684\u4f7f\u7528\u6559\u7a0b\uff0c\u5305\u62ec\u4e0b\u6e38\u6570\u636e\u5904\u7406\u4ee5\u53ca\u5dee\u5f02\u5bcc\u96c6\u5206\u6790\u7b49\uff0c\u5e0c\u671b\u5c0f\u679c\u53ef\u4ee5\u5e2e\u52a9\u5230\u4f60\uff01<\/span><\/strong><span style=\"letter-spacing: 0.034em;font-size: 14px;\"><\/span><\/p>\n<section powered-by=\"xiumi.us\" style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;text-align: left;\">\n<section style=\"font-size: 16px;\">\n<section powered-by=\"xiumi.us\" style=\"margin: 10px;justify-content: flex-start;display: flex;flex-flow: row;\">\n<section style=\"padding-right: 10px;padding-left: 10px;display: inline-block;width: 558px;vertical-align: top;border-style: dashed;border-width: 1px;border-color: rgb(62, 62, 62);align-self: flex-start;flex: 0 0 auto;\">\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 10px;\">\n<section style=\"display: inline-block;width: 536px;border-width: 0px 0px 0px 10px;border-style: solid;border-left-color: rgb(144, 215, 236);border-right-color: rgb(46, 172, 109);box-shadow: rgb(0, 0, 0) 0px 0px 0px;border-bottom-left-radius: 0px;\">\n<section powered-by=\"xiumi.us\" style=\"padding-right: 3px;padding-left: 3px;\">\n<section style=\"margin-top: 0.95em;margin-bottom: -0.65em;display: inline-block;width: 520px;vertical-align: top;\">\n<section style=\"margin-top: -1em;padding: 3px 10px;display: inline-block;vertical-align: top;background-color: rgb(255, 255, 255);color: rgb(0, 154, 68);\">\n<p><strong>\u5f80\u671f\u63a8\u8350<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"text-align: justify;\">\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491794&idx=1&sn=2b7a4de95169c79202e44813885a8250&chksm=cf7f7017f808f9015689839fe4057fd418bf7b20eb1dfb5a28cd92e56a41b5605e62bfbc16fb&scene=21#wechat_redirect\" textvalue=\"1.\u642d\u5efa\u751f\u4fe1\u5206\u6790\u6d41\u6c34\u7ebf\uff0c\u5982\u5de5\u5382\u4e00\u683724\u5c0f\u65f6\u8fd0\u8f6cSnakemake\u2014\u2014\u8fdb\u9636\u547d\u4ee4\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" style=\"font-size: 14px;\" rel=\"noopener\">1.\u642d\u5efa\u751f\u4fe1\u5206\u6790\u6d41\u6c34\u7ebf\uff0c\u5982\u5de5\u5382\u4e00\u683724\u5c0f\u65f6\u8fd0\u8f6cSnakemake\u2014\u2014\u8fdb\u9636\u547d\u4ee4<\/a><br \/><\/section>\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491705&idx=1&sn=9ff9b6da28b3a256a99c6697d589be66&chksm=cf7f70bcf808f9aafd1019a0bba3dd3a55e2867dbb9a09203f13c2683adf867094637c405ed1&scene=21#wechat_redirect\" textvalue=\"2.\u6bd4blast\u8fd8\u4f18\u79c0\u7684\u5e8f\u5217\u6bd4\u5bf9\u5de5\u5177\uff1fHMMER\u6765\u4e86\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" style=\"font-size: 14px;\" rel=\"noopener\">2.\u6bd4blast\u8fd8\u4f18\u79c0\u7684\u5e8f\u5217\u6bd4\u5bf9\u5de5\u5177\uff1fHMMER\u6765\u4e86<\/a><\/section>\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491909&idx=1&sn=902e34bcf53e605fba2b457ec6a33e36&chksm=cf7f7180f808f8961542f458a49da14e85d8831449fb65fbf2623d55affc564686a5422f56fd&scene=21#wechat_redirect\" textvalue=\"3.\u5bf9\u5355\u7ec6\u80de\u5206\u6790\u6beb\u65e0\u5934\u7eea\uff1f\u8ba9popsicleR\u9886\u4f60\u5165\u95e8\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" style=\"font-size: 14px;\" rel=\"noopener\">3.\u5bf9\u5355\u7ec6\u80de\u5206\u6790\u6beb\u65e0\u5934\u7eea\uff1f\u8ba9popsicleR\u9886\u4f60\u5165\u95e8<\/a><\/section>\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491905&idx=1&sn=fb34ebd6282962c7803badaee7a39096&chksm=cf7f7184f808f8929608c0050344ad86193d0fc6455c1c18e16cc17bf4b37832b63d3b18284e&scene=21#wechat_redirect\" textvalue=\"4.\u5c0f\u679c\u5e26\u4f60\u7ed8\u5236ROC\u66f2\u7ebf\u8bc4\u4f30\u751f\u5b58\u9884\u6d4b\u80fd\u529b\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" rel=\"noopener\"><span style=\"font-size: 14px;\">4.\u5c0f\u679c\u5e26\u4f60\u7ed8\u5236ROC\u66f2\u7ebf\u8bc4\u4f30\u751f\u5b58\u9884\u6d4b\u80fd\u529b<\/span><\/a><\/section>\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247493633&idx=1&sn=2263dfe7572c0bcf6816c2c1a37d79de&chksm=cf7f78c4f808f1d2209321d6ace39fde5fa60c0691b56f88eac21916f5a2872ce8ee345f1d5f&scene=21#wechat_redirect\" textvalue=\"\u8f6f\u4ef6\u5305\u5b89\u88c5\u3001\u6253\u602a\u5feb\u53c8\u597d\uff0c1024G\u5b58\u50a8\u7684\u751f\u4fe1\u670d\u52a1\u5668\uff1b\u8fd8\u6709\u6bd4\u8fd9\u66f4\u7701\u94b1\u7684\u561b\uff01\uff01\uff01\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" style=\"letter-spacing: 0.578px;font-size: 14px;\" rel=\"noopener\">5.\u8f6f\u4ef6\u5305\u5b89\u88c5\u3001\u6253\u602a\u5feb\u53c8\u597d\uff0c1024G\u5b58\u50a8\u7684\u751f\u4fe1\u670d\u52a1\u5668\uff1b\u8fd8\u6709\u6bd4\u8fd9\u66f4\u7701\u94b1\u7684\u561b\uff01\uff01\uff01<\/a><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;text-align: left;\"><span style=\"font-size: 10.5pt;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247493633&idx=1&sn=2263dfe7572c0bcf6816c2c1a37d79de&chksm=cf7f78c4f808f1d2209321d6ace39fde5fa60c0691b56f88eac21916f5a2872ce8ee345f1d5f&scene=21#wechat_redirect\" textvalue=\"\u4f60\u5df2\u9009\u4e2d\u4e86\u6dfb\u52a0\u94fe\u63a5\u7684\u5185\u5bb9\" linktype=\"text\" 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