{"id":685,"date":"2021-03-16T09:43:04","date_gmt":"2021-03-16T01:43:04","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=685"},"modified":"2021-04-02T09:30:00","modified_gmt":"2021-04-02T01:30:00","slug":"limma%e5%8e%bb%e9%99%a4%e6%89%b9%e6%ac%a1%e6%95%88%e5%ba%94","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=685","title":{"rendered":"limma\u53bb\u9664\u6279\u6b21\u6548\u5e94"},"content":{"rendered":"<p>\u4ec0\u4e48\u662f\u6279\u6b21\u6548\u5e94\uff08batch effect\uff09\uff1f<br \/>\u4e0d\u540c\u5e73\u53f0\u7684\u6570\u636e\uff0c\u540c\u4e00\u5e73\u53f0\u7684\u4e0d\u540c\u65f6\u671f\u7684\u6570\u636e\uff0c\u540c\u4e00\u4e2a\u6837\u54c1\u4e0d\u540c\u8bd5\u5242\u7684\u6570\u636e\uff0c\u4ee5\u53ca\u540c\u4e00\u4e2a\u6837\u54c1\u4e0d\u540c\u65f6\u95f4\u7684\u6570\u636e\u7b49\u7b49\u90fd\u4f1a\u4ea7\u751f\u4e00\u79cdbatch effect \u3002\u8fd9\u79cd\u5f71\u54cd\u5982\u679c\u5e7f\u6cdb\u5b58\u5728\u5e94\u8be5\u88ab\u8db3\u591f\u91cd\u89c6\uff0c\u5426\u5219\u4f1a\u5bfc\u81f4\u6574\u4e2a\u5b9e\u9a8c\u548c\u6700\u7ec8\u7684\u7ed3\u8bba\u5931\u8d25\u3002\u6bd4\u5bf9\u5b9e\u9a8c\u7ec4\u548c\u5bf9\u7167\u7ec4\uff0c\u4e0d\u540c\u7684\u5904\u7406\u662f\u60a3\u75c5\u548c\u4e0d\u60a3\u75c5\uff08\u6d4b\u5e8f\u65f6\uff0c\u5148\u6d4b\u5f97\u75be\u75c5\uff0c\u7136\u540e\u6d4b\u5f97\u6b63\u5e38\uff09\uff0c\u7136\u540e\u4f60\u901a\u8fc7\u5206\u6790\uff0c\u5f97\u5230\u5f88\u591a\u5dee\u5f02\u8868\u8fbe\u7684\u57fa\u56e0\u3002\u73b0\u5728\u95ee\u9898\u6765\u4e86\uff0c\u8fd9\u4e2a\u5dee\u5f02\u8868\u8fbe\u7684\u7ed3\u679c\u662f\u548c\u4f60\u8981\u7814\u7a76\u7684\u56e0\u7d20\u6709\u5173\uff0c\u8fd8\u662f\u65f6\u95f4\u6709\u5173\uff0c\u8fd9\u4e2a\u95ee\u9898\u91cc\u65f6\u95f4\u5c31\u4f1a\u6210\u4e3a\u5e72\u6270\u5b9e\u9a8c\u7ed3\u679c\u7684\u56e0\u7d20\uff0c\u8fd9\u4e2a\u6548\u5e94\u5c31\u662fbatch effect\u3002<\/p>\n<pre>library(limma)\ndata &lt;- read.table(\"mouse_gc.xls\",sep=\"\\t\",header = TRUE)\nbatch1 &lt;- c(rep('fish',9),rep('mouse',9))\nbatch1 &lt;- as.factor(batch1)\ndesign &lt;- model.matrix(~0 + batch1)<br \/>#data=normalizeBetweenArrays(data)#\u5982\u679c\u7ec4\u5185\u7684\u4e2d\u4f4d\u6570\u4e0d\u5728\u540c\u4e00\u6761\u6c34\u5e73\u7ebf\u4e0a\uff0c\u73b0\u5728\u8be5\u53c2\u6570\u6821\u6b63\uff0c\u518d\u4f7f\u7528\u4e0b\u9762\u7684\u6279\u6b21\u6821\u6b63\nnew_data &lt;- removeBatchEffect(data[,2:19], batch = batch1)\nboxplot(data[,2:19])\nboxplot(new_data)\nwrite.table(new_data, file=\"removeBatch.xls\", sep=\"\\t\", quote=F, row.names=T, col.names=T)<\/pre>\n<p>limma\u7ed3\u679c\u51fa\u73b0\u8d1f\u503c\u8bf7\u53c2\u8003\uff1a<a href=\"https:\/\/cloud.tencent.com\/developer\/article\/1680305\">https:\/\/cloud.tencent.com\/developer\/article\/1680305<\/a><br \/>\u53c2\u8003\u94fe\u63a5\uff1a<a href=\"https:\/\/www.omicsclass.com\/article\/1113\">https:\/\/www.omicsclass.com\/article\/1113<\/a><\/p>\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u4ec0\u4e48\u662f\u6279\u6b21\u6548\u5e94\uff08batch effect\uff09\uff1f\u4e0d\u540c\u5e73\u53f0\u7684\u6570\u636e\uff0c\u540c\u4e00\u5e73\u53f0\u7684\u4e0d\u540c\u65f6\u671f\u7684\u6570\u636e\uff0c\u540c\u4e00\u4e2a\u6837\u54c1\u4e0d\u540c\u8bd5\u5242\u7684\u6570\u636e\uff0c\u4ee5\u53ca\u540c\u4e00\u4e2a\u6837\u54c1\u4e0d\u540c\u65f6\u95f4\u7684\u6570\u636e\u7b49\u7b49\u90fd\u4f1a\u4ea7\u751f\u4e00\u79cdbatch effect \u3002\u8fd9\u79cd\u5f71\u54cd\u5982\u679c\u5e7f\u6cdb\u5b58\u5728\u5e94\u8be5\u88ab\u8db3\u591f\u91cd\u89c6\uff0c\u5426\u5219\u4f1a\u5bfc\u81f4\u6574\u4e2a\u5b9e\u9a8c\u548c\u6700\u7ec8\u7684\u7ed3\u8bba\u5931\u8d25\u3002\u6bd4\u5bf9\u5b9e\u9a8c\u7ec4\u548c\u5bf9\u7167\u7ec4\uff0c\u4e0d\u540c\u7684\u5904\u7406\u662f\u60a3\u75c5\u548c\u4e0d\u60a3\u75c5\uff08\u6d4b\u5e8f\u65f6\uff0c\u5148\u6d4b\u5f97\u75be\u75c5\uff0c\u7136\u540e\u6d4b\u5f97\u6b63\u5e38\uff09\uff0c\u7136\u540e\u4f60\u901a\u8fc7\u5206\u6790\uff0c\u5f97\u5230\u5f88\u591a\u5dee\u5f02\u8868\u8fbe\u7684\u57fa\u56e0\u3002\u73b0\u5728\u95ee\u9898\u6765\u4e86\uff0c\u8fd9\u4e2a\u5dee\u5f02\u8868\u8fbe\u7684\u7ed3\u679c\u662f\u548c\u4f60\u8981\u7814\u7a76\u7684\u56e0\u7d20\u6709\u5173\uff0c\u8fd8\u662f\u65f6\u95f4\u6709\u5173\uff0c\u8fd9\u4e2a\u95ee\u9898\u91cc\u65f6\u95f4\u5c31\u4f1a\u6210\u4e3a\u5e72\u6270\u5b9e\u9a8c\u7ed3\u679c\u7684\u56e0\u7d20\uff0c\u8fd9\u4e2a\u6548\u5e94\u5c31\u662fbatch effect\u3002 library(limma) data &lt;- read.table(&#8220;mouse_gc.xls&#8221;,sep=&#8221;\\t&#8221;,header = TRUE) batch1 &lt;- c(rep(&#8216;fish&#8217;,9),rep(&#8216;mouse&#8217;,9)) batch1 &lt;- as.factor(batch1) design &lt;- model.matrix(~0 + batch1)#data=normalizeBetweenArrays(data)#\u5982\u679c\u7ec4\u5185\u7684\u4e2d\u4f4d\u6570\u4e0d\u5728\u540c\u4e00\u6761\u6c34\u5e73\u7ebf\u4e0a\uff0c\u73b0\u5728\u8be5\u53c2\u6570\u6821\u6b63\uff0c\u518d\u4f7f\u7528\u4e0b\u9762\u7684\u6279\u6b21\u6821\u6b63 new_data &lt;- removeBatchEffect(data[,2:19], batch = batch1) boxplot(data[,2:19]) boxplot(new_data) write.table(new_data, file=&#8221;removeBatch.xls&#8221;, sep=&#8221;\\t&#8221;, quote=F, row.names=T, col.names=T) limma\u7ed3\u679c\u51fa\u73b0\u8d1f\u503c\u8bf7\u53c2\u8003\uff1ahttps:\/\/cloud.tencent.com\/developer\/article\/1680305\u53c2\u8003\u94fe\u63a5\uff1ahttps:\/\/www.omicsclass.com\/article\/1113<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4,10],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/685"}],"collection":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=685"}],"version-history":[{"count":4,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/685\/revisions"}],"predecessor-version":[{"id":733,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/685\/revisions\/733"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=685"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=685"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=685"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}