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onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/zcicibWZessAxZibD6iaowp2Zv5dgyZQqBVAac9npnibJvGYo1ZFiafpiayXgbaYHrH5kBzN1unDT7eHqLtdZO1vwdtrw\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<section style=\"box-sizing: border-box;font-size: 16px;\">\n<section style=\"box-sizing: border-box;font-size: 16px;\">\n<section style=\"transform-origin: right top;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"box-sizing: border-box;font-size: 16px;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;background-color: rgba(255, 255, 255, 0.83);align-self: flex-start;flex: 0 0 auto;box-sizing: border-box;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;padding: 28px 28px 7px;align-self: flex-start;flex: 0 0 auto;background-color: rgb(255, 248, 248);box-sizing: border-box;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: -25px;margin-bottom: 10px;transform: translate3d(-25px, 0px, 0px);box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 1px;border-color: rgb(207, 65, 61);min-width: 5%;max-width: 100%;height: auto;padding: 11px;box-sizing: border-box;\">\n<section style=\"margin-top: -10px;margin-bottom: -10px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: justify;box-sizing: border-box;\">\n<p style=\"white-space: normal;box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">GEO2R<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;max-width: 100%;flex: 0 0 auto;height: auto;align-self: flex-end;box-sizing: border-box;\">\n<section style=\"transform: perspective(0px);-webkit-transform: perspective(0px);-moz-transform: perspective(0px);-o-transform: perspective(0px);transform-style: flat;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"transform: translate3d(-8px, 0px, 0px) rotateX(180deg);-webkit-transform: translate3d(-8px, 0px, 0px) rotateX(180deg);-moz-transform: translate3d(-8px, 0px, 0px) rotateX(180deg);-o-transform: translate3d(-8px, 0px, 0px) rotateX(180deg);box-sizing: border-box;\">\n<section style=\"display: inline-block;width: 18px;height: 18px;vertical-align: top;overflow: hidden;background-color: rgb(207, 65, 61);box-sizing: border-box;\">\n<section style=\"text-align: justify;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\">\u4ee5GSE70493\u4e3a\u4f8b\uff0c\u8fdb\u884cR\u4ee3\u7801\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u53ef\u89c6\u5316\u5206\u6790\u5b66\u4e60\uff1a<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># Visualize and quality control test results.<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># Build histogram of P-values for all genes. Normal test<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># assumption is that most genes are not differentially expressed.<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">tT2 <- topTable(fit2, adjust=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"fdr\"<\/span>, sort.by=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"B\"<\/span>, number=<span class=\"code-snippet__literal\" style=\"box-sizing: border-box;\">Inf<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">hist(tT2$adj.P.Val, col = <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"grey\"<\/span>, border = <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"white\"<\/span>, xlab = <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"P-adj\"<\/span>,<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">ylab = <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"Number of genes\"<\/span>, main = <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"P-adj value distribution\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u5bf9\u6240\u6709\u57fa\u56e0\u8fdb\u884c\u76f4\u65b9\u56fe\u7ed8\u5236\uff0chist\u5904\u662f\u7ed8\u5236\u76f4\u65b9\u56fe\u7684\u547d\u4ee4\uff0ccol : \u67f1\u5b50\u7684\u586b\u5145\u8272 \uff0cborder\uff1a\u5b50\u7684\u8fb9\u6846\u7684\u989c\u8272\uff0cxlab\uff1ax\u8f74\u540d\u79f0\uff0c ylab\uff1ay\u8f74\u540d\u79f0\uff0cmain\uff1a\u76f4\u65b9\u56fe\u6807\u9898\u540d\u79f0\u3002<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># summarize test results as \"up\", \"down\" or \"not expressed\"<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">dT <- decideTests(fit2, adjust.method=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"fdr\"<\/span>, p.value=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0.05<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u901a\u8fc7decideTests\u51fd\u6570\u8ba1\u7b97\u53bb\u7edf\u8ba1\u5dee\u5f02\u57fa\u56e0\u7684\u8868\u8fbe\u60c5\u51b5\u3002<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># Venn diagram of results<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">vennDiagram(dT, circle.col=palette())<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u5bf9\u5dee\u5f02\u7ed3\u679c\u8fdb\u884cvenn\u56fe\u7ed8\u5236\uff0c\u7ed8\u56fe\u4f7f\u7528\u7684\u51fd\u6570\u662fvennDiagram\u51fd\u6570<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># create Q-Q plot for t-statistic<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">t.good <- which(!<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">is.na<\/span>(fit2$<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">F<\/span>)) <span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># filter out bad probes<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">qqt(fit2$t[t.good], fit2$df.total[t.good], main=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"Moderated t statistic\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u5bf9\u6570\u636e\u8fdb\u884ct\u68c0\u9a8c\uff0cQ\u2013Q (quantile-quantile) plot \u5373\u7ed8\u5236\u6563\u70b9\u56fe<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># volcano plot (log P-value vs log fold change)<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">colnames(fit2) <span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># list contrast names<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">ct <- 1 <span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># choose contrast of interest<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">volcanoplot(fit2, coef=ct, main=colnames(fit2)[ct], pch=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">20<\/span>,<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">highlight=<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">length<\/span>(which(dT[,ct]!=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0<\/span>)), <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">names<\/span>=<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">rep<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'+'<\/span>, nrow(fit2)))<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u4f7f\u7528log P-value\u548c\uff0clog fold change\u503c\u8fdb\u884c\u706b\u5c71\u56fe\u7ed8\u5236\uff0c\u9996\u5148\u5217\u51fa\u4e86\u7ec4\u540d\uff0c\u7136\u540e\u9009\u62e9\u4e00\u70b9\u611f\u5174\u8da3\u7684\u7ec4\u8fdb\u884c\u706b\u5c71\u56fe\u7684\u7ed8\u5236\uff0c\u706b\u5c71\u56fe\u7684\u7ed8\u56fe\u4f7f\u7528\u7684\u662fvolcanoplot\u51fd\u6570\u3002<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># MD plot (log fold change vs mean log expression)<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># highlight statistically significant (p-adj < 0.05) probes<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">plotMD(fit2, column=ct, status=dT[,ct], legend=<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">F<\/span>, pch=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">20<\/span>, cex=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">abline(h=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u5e73\u5747\u5dee\u5f02\u56fe(MD-plot)\u662f\u5bf9\u6570\u6298\u53e0\u53d8\u5316(\u5dee\u5f02)\u4e0e\u5e73\u5747\u5bf9\u6570\u503c(\u5e73\u5747\u503c)\u7684\u66f2\u7ebf\u3002\u5728\u6b64\u5904\u8fdb\u884c\u5f3a\u8c03\u7edf\u8ba1\u663e\u8457\u6027(\u5373p-adj <0.05)\uff0c\u7ed8\u56fe\u6240\u7528\u51fd\u6570\u662fpoltMD\u51fd\u6570 \u3002<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># General expression data analysis<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">ex <- exprs(gset)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u63d0\u53d6\u4e86\u5dee\u5f02\u8868\u8fbe\u6570\u636e\uff0c\u8fdb\u884c\u8868\u8fbe\u6570\u636e\u7684\u5206\u6790<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># box-and-whisker plot<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">dev.new(width=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">3<\/span>+ncol(gset)\/<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">6<\/span>, height=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">5<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">ord <- order(gs) <span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># order samples by group<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">palette(<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#1B9E77\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#7570B3\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#E7298A\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#E6AB02\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#D95F02\"<\/span>,<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\"><span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#66A61E\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#A6761D\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#B32424\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#B324B3\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#666666\"<\/span>))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">par(mar=<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">7<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">4<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">title <- paste (<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"GSE70493\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"\/\"<\/span>, annotation(gset), sep =<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"\"<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">boxplot(ex[,ord], boxwex=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0.6<\/span>, notch=<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">T<\/span>, main=title, outline=<span class=\"code-snippet__literal\" style=\"box-sizing: border-box;\">FALSE<\/span>, las=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>, col=gs[ord])<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">legend(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"topleft\"<\/span>, groups, fill=palette(), bty=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"n\"<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u8fdb\u884c\u7bb1\u7ebf\u56fe\u7684\u7ed8\u5236\uff0c\u5b83\u662f\u4e00\u79cd\u7528\u4f5c\u663e\u793a\u4e00\u7ec4\u6570\u636e\u5206\u6563\u60c5\u51b5\u8d44\u6599\u7684\u7edf\u8ba1\u56fe\uff0c \u4f7f\u7528boxplot\u51fd\u6570\u8fdb\u884c\u7ed8\u5236\uff0cdev.new\u6253\u5f00\u7ed8\u56fe\u6a21\u5f0f\uff0cdev.offff()\u5173\u95ed\u7ed8\u56fe\u6a21\u5f0f<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># expression value distribution<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">par(mar=<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">4<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">4<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">title <- paste (<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"GSE70493\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"\/\"<\/span>, annotation(gset), <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\" value distribution\"<\/span>, sep =<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"\"<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">plotDensities(ex, group=gs, main=title, legend =<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"topright\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u7edf\u8ba1\u8868\u8fbe\u5f0f\u503c\u5e76\u7ed8\u5236\u5206\u5e03\u5bc6\u5ea6\u56fe \uff0c\u8fd9\u91cc\u7528\u5230\u4e86plotDensities\u51fd\u6570\uff0c\u5305\u542b\u8868\u8fbe\u77e9\u9635\uff0c\u5206\u7ec4\u60c5\u51b5\uff0c\u6807\u9898\u540d\u79f0\u7b49\u4fe1\u606f\u3002<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># mean-variance trend, helps to see if precision weights are needed<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">plotSA(fit2, main=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"Mean variance trend, GSE70493\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u7ed8\u5236\u662f\u5e73\u5747\u65b9\u5dee\u8d8b\u52bf\u56fe\uff0c\u4f7f\u7528plotSA\u51fd\u6570\uff0c\u76ee\u7684\u662f\u4e3a\u4e86\u660e\u786e\u662f\u5426\u9700\u8981\u53bb\u8ba1\u7b97\u6743\u91cd\u3002<span style=\"text-align: right;\"><\/span><\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"box-sizing: border-box;font-size: 16px;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: stretch;flex: 0 0 auto;background-color: rgb(226, 91, 91);min-width: 5%;max-width: 100%;height: auto;padding-top: 5px;padding-right: 9px;padding-left: 20px;box-sizing: border-box;\">\n<section style=\"text-align: justify;color: rgb(255, 255, 255);box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">\u626b\u7801\u5173\u6ce8\u6211\u4eec<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;max-width: 100%;flex: 0 0 auto;height: auto;align-self: stretch;box-sizing: border-box;\">\n<section style=\"box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 0px;height: 0px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 38px 0px 0px 19px;border-color: rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgb(226, 91, 91);box-sizing: border-box;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 20px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: 37%;align-self: center;flex: 0 0 auto;height: auto;box-sizing: border-box;\">\n<section style=\"text-align: center;margin-top: 10px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;width: 90%;height: auto;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_89OwvlQm3aO2ML1v1qDzHNWAic9Tcg.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/zcicibWZessAwMHt5r1zOwBibker7jibV7yMuXX4P2dGIZhJQMKztBmhgNtxr89OwvlQm3aO2ML1v1qDzHNWAic9Tcg\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"344\" style=\"vertical-align: middle;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 57%;align-self: center;flex: 0 0 auto;height: auto;box-sizing: border-box;\">\n<section style=\"text-align: right;margin-bottom: 4px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"color: rgb(238, 216, 190);box-sizing: border-box;\">\n<p style=\"box-sizing: border-box;\">shengxinguoer<\/p>\n<\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: -4px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: right;color: rgb(226, 91, 91);font-size: 23px;line-height: 1.1;box-sizing: border-box;\">\n<p style=\"box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">\u751f\u4fe1\u679c<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<\/section>\n<section style=\"text-align: center;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: right;box-sizing: border-box;\">\n<p style=\"box-sizing: border-box;\">\u751f\u4fe1\u786c\u6838\u77e5\u8bc6\u89e3\u7b54<\/p>\n<p style=\"box-sizing: border-box;\">\u548c\u5c0f\u679c\u4e00\u8d77\u5b66\u751f\u4fe1<\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"display: none;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<p><\/content>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>GEO2R\u5206\u6790R\u4ee3\u7801\u5b66\u4e60\u4e4b\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u53ef\u89c6\u5316 \u539f\u521b \u5c0f\u679c \u751f\u4fe1\u679c& 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{"id":48381,"date":"2024-06-15T20:08:09","date_gmt":"2024-06-15T12:08:09","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=48381"},"modified":"2024-06-15T20:08:09","modified_gmt":"2024-06-15T12:08:09","slug":"geo2r%e5%88%86%e6%9e%90r%e4%bb%a3%e7%a0%81%e5%ad%a6%e4%b9%a0%e4%b9%8b%e5%b7%ae%e5%bc%82%e5%88%86%e6%9e%90%e7%bb%93%e6%9e%9c%e5%8f%af%e8%a7%86%e5%8c%96","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=48381","title":{"rendered":"GEO2R\u5206\u6790R\u4ee3\u7801\u5b66\u4e60\u4e4b\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u53ef\u89c6\u5316"},"content":{"rendered":"

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onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/zcicibWZessAxZibD6iaowp2Zv5dgyZQqBVAac9npnibJvGYo1ZFiafpiayXgbaYHrH5kBzN1unDT7eHqLtdZO1vwdtrw\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<section style=\"box-sizing: border-box;font-size: 16px;\">\n<section style=\"box-sizing: border-box;font-size: 16px;\">\n<section style=\"transform-origin: right top;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"box-sizing: border-box;font-size: 16px;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 10px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;background-color: rgba(255, 255, 255, 0.83);align-self: flex-start;flex: 0 0 auto;box-sizing: border-box;\">\n<section style=\"justify-content: flex-start;display: flex;flex-flow: row nowrap;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;padding: 28px 28px 7px;align-self: flex-start;flex: 0 0 auto;background-color: rgb(255, 248, 248);box-sizing: border-box;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: -25px;margin-bottom: 10px;transform: translate3d(-25px, 0px, 0px);box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 1px;border-color: rgb(207, 65, 61);min-width: 5%;max-width: 100%;height: auto;padding: 11px;box-sizing: border-box;\">\n<section style=\"margin-top: -10px;margin-bottom: -10px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: justify;box-sizing: border-box;\">\n<p style=\"white-space: normal;box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">GEO2R<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;max-width: 100%;flex: 0 0 auto;height: auto;align-self: flex-end;box-sizing: border-box;\">\n<section style=\"transform: perspective(0px);-webkit-transform: perspective(0px);-moz-transform: perspective(0px);-o-transform: perspective(0px);transform-style: flat;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"transform: translate3d(-8px, 0px, 0px) rotateX(180deg);-webkit-transform: translate3d(-8px, 0px, 0px) rotateX(180deg);-moz-transform: translate3d(-8px, 0px, 0px) rotateX(180deg);-o-transform: translate3d(-8px, 0px, 0px) rotateX(180deg);box-sizing: border-box;\">\n<section style=\"display: inline-block;width: 18px;height: 18px;vertical-align: top;overflow: hidden;background-color: rgb(207, 65, 61);box-sizing: border-box;\">\n<section style=\"text-align: justify;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\">\u4ee5GSE70493\u4e3a\u4f8b\uff0c\u8fdb\u884cR\u4ee3\u7801\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u53ef\u89c6\u5316\u5206\u6790\u5b66\u4e60\uff1a<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># Visualize and quality control test results.<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># Build histogram of P-values for all genes. Normal test<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># assumption is that most genes are not differentially expressed.<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">tT2 <- topTable(fit2, adjust=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"fdr\"<\/span>, sort.by=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"B\"<\/span>, number=<span class=\"code-snippet__literal\" style=\"box-sizing: border-box;\">Inf<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">hist(tT2$adj.P.Val, col = <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"grey\"<\/span>, border = <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"white\"<\/span>, xlab = <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"P-adj\"<\/span>,<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">ylab = <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"Number of genes\"<\/span>, main = <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"P-adj value distribution\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u5bf9\u6240\u6709\u57fa\u56e0\u8fdb\u884c\u76f4\u65b9\u56fe\u7ed8\u5236\uff0chist\u5904\u662f\u7ed8\u5236\u76f4\u65b9\u56fe\u7684\u547d\u4ee4\uff0ccol : \u67f1\u5b50\u7684\u586b\u5145\u8272 \uff0cborder\uff1a\u5b50\u7684\u8fb9\u6846\u7684\u989c\u8272\uff0cxlab\uff1ax\u8f74\u540d\u79f0\uff0c ylab\uff1ay\u8f74\u540d\u79f0\uff0cmain\uff1a\u76f4\u65b9\u56fe\u6807\u9898\u540d\u79f0\u3002<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># summarize test results as \"up\", \"down\" or \"not expressed\"<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">dT <- decideTests(fit2, adjust.method=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"fdr\"<\/span>, p.value=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0.05<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u901a\u8fc7decideTests\u51fd\u6570\u8ba1\u7b97\u53bb\u7edf\u8ba1\u5dee\u5f02\u57fa\u56e0\u7684\u8868\u8fbe\u60c5\u51b5\u3002<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># Venn diagram of results<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">vennDiagram(dT, circle.col=palette())<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u5bf9\u5dee\u5f02\u7ed3\u679c\u8fdb\u884cvenn\u56fe\u7ed8\u5236\uff0c\u7ed8\u56fe\u4f7f\u7528\u7684\u51fd\u6570\u662fvennDiagram\u51fd\u6570<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># create Q-Q plot for t-statistic<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">t.good <- which(!<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">is.na<\/span>(fit2$<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">F<\/span>)) <span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># filter out bad probes<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">qqt(fit2$t[t.good], fit2$df.total[t.good], main=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"Moderated t statistic\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u5bf9\u6570\u636e\u8fdb\u884ct\u68c0\u9a8c\uff0cQ\u2013Q (quantile-quantile) plot \u5373\u7ed8\u5236\u6563\u70b9\u56fe<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># volcano plot (log P-value vs log fold change)<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">colnames(fit2) <span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># list contrast names<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">ct <- 1 <span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># choose contrast of interest<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">volcanoplot(fit2, coef=ct, main=colnames(fit2)[ct], pch=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">20<\/span>,<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">highlight=<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">length<\/span>(which(dT[,ct]!=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0<\/span>)), <span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">names<\/span>=<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">rep<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">'+'<\/span>, nrow(fit2)))<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u4f7f\u7528log P-value\u548c\uff0clog fold change\u503c\u8fdb\u884c\u706b\u5c71\u56fe\u7ed8\u5236\uff0c\u9996\u5148\u5217\u51fa\u4e86\u7ec4\u540d\uff0c\u7136\u540e\u9009\u62e9\u4e00\u70b9\u611f\u5174\u8da3\u7684\u7ec4\u8fdb\u884c\u706b\u5c71\u56fe\u7684\u7ed8\u5236\uff0c\u706b\u5c71\u56fe\u7684\u7ed8\u56fe\u4f7f\u7528\u7684\u662fvolcanoplot\u51fd\u6570\u3002<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># MD plot (log fold change vs mean log expression)<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># highlight statistically significant (p-adj < 0.05) probes<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">plotMD(fit2, column=ct, status=dT[,ct], legend=<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">F<\/span>, pch=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">20<\/span>, cex=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">abline(h=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u5e73\u5747\u5dee\u5f02\u56fe(MD-plot)\u662f\u5bf9\u6570\u6298\u53e0\u53d8\u5316(\u5dee\u5f02)\u4e0e\u5e73\u5747\u5bf9\u6570\u503c(\u5e73\u5747\u503c)\u7684\u66f2\u7ebf\u3002\u5728\u6b64\u5904\u8fdb\u884c\u5f3a\u8c03\u7edf\u8ba1\u663e\u8457\u6027(\u5373p-adj <0.05)\uff0c\u7ed8\u56fe\u6240\u7528\u51fd\u6570\u662fpoltMD\u51fd\u6570 \u3002<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># General expression data analysis<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">ex <- exprs(gset)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u63d0\u53d6\u4e86\u5dee\u5f02\u8868\u8fbe\u6570\u636e\uff0c\u8fdb\u884c\u8868\u8fbe\u6570\u636e\u7684\u5206\u6790<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># box-and-whisker plot<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">dev.new(width=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">3<\/span>+ncol(gset)\/<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">6<\/span>, height=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">5<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\">ord <- order(gs) <span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># order samples by group<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">palette(<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#1B9E77\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#7570B3\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#E7298A\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#E6AB02\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#D95F02\"<\/span>,<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\"><span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#66A61E\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#A6761D\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#B32424\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#B324B3\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"#666666\"<\/span>))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">par(mar=<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">7<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">4<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">title <- paste (<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"GSE70493\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"\/\"<\/span>, annotation(gset), sep =<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"\"<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">boxplot(ex[,ord], boxwex=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">0.6<\/span>, notch=<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">T<\/span>, main=title, outline=<span class=\"code-snippet__literal\" style=\"box-sizing: border-box;\">FALSE<\/span>, las=<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>, col=gs[ord])<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">legend(<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"topleft\"<\/span>, groups, fill=palette(), bty=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"n\"<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u8fdb\u884c\u7bb1\u7ebf\u56fe\u7684\u7ed8\u5236\uff0c\u5b83\u662f\u4e00\u79cd\u7528\u4f5c\u663e\u793a\u4e00\u7ec4\u6570\u636e\u5206\u6563\u60c5\u51b5\u8d44\u6599\u7684\u7edf\u8ba1\u56fe\uff0c \u4f7f\u7528boxplot\u51fd\u6570\u8fdb\u884c\u7ed8\u5236\uff0cdev.new\u6253\u5f00\u7ed8\u56fe\u6a21\u5f0f\uff0cdev.offff()\u5173\u95ed\u7ed8\u56fe\u6a21\u5f0f<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># expression value distribution<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">par(mar=<span class=\"code-snippet__built_in\" style=\"box-sizing: border-box;\">c<\/span>(<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">4<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">4<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">2<\/span>,<span class=\"code-snippet__number\" style=\"box-sizing: border-box;\">1<\/span>))<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">title <- paste (<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"GSE70493\"<\/span>, <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"\/\"<\/span>, annotation(gset), <span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\" value distribution\"<\/span>, sep =<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"\"<\/span>)<\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">plotDensities(ex, group=gs, main=title, legend =<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"topright\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u662f\u7edf\u8ba1\u8868\u8fbe\u5f0f\u503c\u5e76\u7ed8\u5236\u5206\u5e03\u5bc6\u5ea6\u56fe \uff0c\u8fd9\u91cc\u7528\u5230\u4e86plotDensities\u51fd\u6570\uff0c\u5305\u542b\u8868\u8fbe\u77e9\u9635\uff0c\u5206\u7ec4\u60c5\u51b5\uff0c\u6807\u9898\u540d\u79f0\u7b49\u4fe1\u606f\u3002<\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\" style=\"box-sizing: border-box;\"><span class=\"code-snippet__comment\" style=\"box-sizing: border-box;\"># mean-variance trend, helps to see if precision weights are needed<\/span><\/span><\/code><code style=\"box-sizing: border-box;\"><span class=\"code-snippet_outer\">plotSA(fit2, main=<span class=\"code-snippet__string\" style=\"box-sizing: border-box;\">\"Mean variance trend, GSE70493\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\">#\u6b64\u6bb5\u4ee3\u7801\u7ed8\u5236\u662f\u5e73\u5747\u65b9\u5dee\u8d8b\u52bf\u56fe\uff0c\u4f7f\u7528plotSA\u51fd\u6570\uff0c\u76ee\u7684\u662f\u4e3a\u4e86\u660e\u786e\u662f\u5426\u9700\u8981\u53bb\u8ba1\u7b97\u6743\u91cd\u3002<span style=\"text-align: right;\"><\/span><\/p>\n<p style=\"white-space: normal;box-sizing: border-box;\" powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"box-sizing: border-box;font-size: 16px;\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: stretch;flex: 0 0 auto;background-color: rgb(226, 91, 91);min-width: 5%;max-width: 100%;height: auto;padding-top: 5px;padding-right: 9px;padding-left: 20px;box-sizing: border-box;\">\n<section style=\"text-align: justify;color: rgb(255, 255, 255);box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">\u626b\u7801\u5173\u6ce8\u6211\u4eec<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;max-width: 100%;flex: 0 0 auto;height: auto;align-self: stretch;box-sizing: border-box;\">\n<section style=\"box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 0px;height: 0px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 38px 0px 0px 19px;border-color: rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgb(226, 91, 91);box-sizing: border-box;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;margin-top: 10px;margin-bottom: 20px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: 37%;align-self: center;flex: 0 0 auto;height: auto;box-sizing: border-box;\">\n<section style=\"text-align: center;margin-top: 10px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"max-width: 100%;vertical-align: middle;display: inline-block;line-height: 0;width: 90%;height: auto;box-sizing: border-box;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_89OwvlQm3aO2ML1v1qDzHNWAic9Tcg.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/zcicibWZessAwMHt5r1zOwBibker7jibV7yMuXX4P2dGIZhJQMKztBmhgNtxr89OwvlQm3aO2ML1v1qDzHNWAic9Tcg\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"344\" style=\"vertical-align: middle;width: 100%;box-sizing: border-box;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 57%;align-self: center;flex: 0 0 auto;height: auto;box-sizing: border-box;\">\n<section style=\"text-align: right;margin-bottom: 4px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"color: rgb(238, 216, 190);box-sizing: border-box;\">\n<p style=\"box-sizing: border-box;\">shengxinguoer<\/p>\n<\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: -4px;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: right;color: rgb(226, 91, 91);font-size: 23px;line-height: 1.1;box-sizing: border-box;\">\n<p style=\"box-sizing: border-box;\"><strong style=\"box-sizing: border-box;\">\u751f\u4fe1\u679c<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"text-align: justify;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;box-sizing: border-box;\"><br style=\"box-sizing: border-box;\" \/><\/p>\n<\/section>\n<section style=\"text-align: center;box-sizing: border-box;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: right;box-sizing: border-box;\">\n<p style=\"box-sizing: border-box;\">\u751f\u4fe1\u786c\u6838\u77e5\u8bc6\u89e3\u7b54<\/p>\n<p style=\"box-sizing: border-box;\">\u548c\u5c0f\u679c\u4e00\u8d77\u5b66\u751f\u4fe1<\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"display: none;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<p><\/content>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>GEO2R\u5206\u6790R\u4ee3\u7801\u5b66\u4e60\u4e4b\u5dee\u5f02\u5206\u6790\u7ed3\u679c\u53ef\u89c6\u5316 \u539f\u521b \u5c0f\u679c \u751f\u4fe1\u679c& 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