{"id":30004,"date":"2024-02-27T18:01:10","date_gmt":"2024-02-27T10:01:10","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=30004"},"modified":"2024-02-27T18:01:12","modified_gmt":"2024-02-27T10:01:12","slug":"%e6%8f%ad%e5%bc%80%e8%82%bf%e7%98%a4%e5%85%8d%e7%96%ab%e5%88%86%e6%9e%90%e7%9a%84%e7%a5%9e%e7%a7%98%e9%9d%a2%e7%ba%b1%ef%bc%9a%e4%bd%bf%e7%94%a8cibersort%e5%88%86%e6%9e%90%e4%bd%a0%e7%9a%84%e5%85%8d","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=30004","title":{"rendered":"\u63ed\u5f00\u80bf\u7624\u514d\u75ab\u5206\u6790\u7684\u795e\u79d8\u9762\u7eb1\uff1a\u4f7f\u7528CIBERSORT\u5206\u6790\u4f60\u7684\u514d\u75ab\u7ec6\u80de\uff01"},"content":{"rendered":"<p><strong>\u63ed\u5f00\u80bf\u7624\u514d\u75ab\u5206\u6790\u7684\u795e\u79d8\u9762\u7eb1\uff1a\u4f7f\u7528CIBERSORT\u5206\u6790\u4f60\u7684\u514d\u75ab\u7ec6\u80de\uff01<\/strong><\/p>\n<p>\u4eca\u5929\uff0c\u5c0f\u679c\u5c06\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u4e00\u4e2a\u57fa\u4e8e\u53cd\u5377\u79ef\u5206\u6790\u7684\u7b97\u6cd5\u53ca\u5176\u5bf9\u5e94\u7684R\u5305\u3002<\/p>\n<p>\u5728\u672c\u6559\u7a0b\u4e2d\uff0c\u6211\u4eec\u5c06\u4f7f\u7528 R \u8bed\u8a00\u4e2d\u7684 CIBERSORT \u5e93\u5bf9\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u8fdb\u884c\u514d\u75ab\u7ec6\u80de\u7c7b\u578b\u7684\u5206\u6790\uff0c\u5e76\u4f7f\u7528 ggplot2 \u5e93\u5bf9\u5206\u6790\u7ed3\u679c\u8fdb\u884c\u53ef\u89c6\u5316\u3002\u90a3\u5c31\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u5427\uff01<\/p>\n<p><strong>\u521d\u8bc6CiberSort<\/strong><\/p>\n<p>\u5728\u5b66\u4e60\u600e\u4e48\u4f7f\u7528\u4e4b\u524d\uff0c\u5c0f\u679c\u6765\u7ed9\u5927\u5bb6\u7b80\u5355\u7684\u4ecb\u7ecd\u4e00\u4e0b\u4ec0\u4e48\u662fCIBERSORT\u3002<\/p>\n<p>CIBERSORT\u662f\u4e00\u79cd\u5e7f\u6cdb\u5e94\u7528\u4e8e\u80bf\u7624\u514d\u75ab\u5b66\u7814\u7a76\u7684\u8ba1\u7b97\u65b9\u6cd5\uff0c\u5b83\u80fd\u591f\u5229\u7528\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u5bf9\u80bf\u7624\u7ec4\u7ec7\u4e2d\u4e0d\u540c\u514d\u75ab\u7ec6\u80de\u4e9a\u7fa4\u7684\u6bd4\u4f8b\u8fdb\u884c\u5b9a\u91cf\u5206\u6790\u3002CIBERSORT\u57fa\u4e8e\u4e00\u4e2a\u7ebf\u6027\u56de\u5f52\u6a21\u578b\uff0c\u8be5\u6a21\u578b\u901a\u8fc7\u5bf9\u5df2\u77e5\u514d\u75ab\u7ec6\u80de\u7279\u5f81\u57fa\u56e0\u8868\u8fbe\u8c31\u7684\u8bad\u7ec3\u6765\u4f30\u8ba1\u6df7\u6742\u7ec6\u80de\u6837\u672c\u4e2d\u5404\u4e2a\u514d\u75ab\u7ec6\u80de\u4e9a\u7fa4\u7684\u76f8\u5bf9\u4e30\u5ea6\u3002<\/p>\n<p>\u597d\u4e86\uff0c\u63a5\u4e0b\u6765\u6211\u4eec\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u600e\u4e48\u4f7f\u7528\u5b83\u5427\uff01<\/p>\n<p><strong>\u6b65\u9aa4 1: \u51c6\u5907\u5de5\u4f5c<\/strong><\/p>\n<p>\u5728\u5f00\u59cb\u5206\u6790\u4e4b\u524d\uff0c\u6211\u4eec\u9700\u8981\u51c6\u5907\u6240\u9700\u7684\u5de5\u5177\u548c\u6570\u636e\u3002\u5177\u4f53\u6765\u8bf4\uff0c\u6211\u4eec\u9700\u8981\u4ee5\u4e0b\u5185\u5bb9\uff1a<\/p>\n<ul>\n<li>\n    \u5b89\u88c5\u4ee5\u4e0b R \u5e93\uff1aggplot2, ggpubr, reshape2, dplyr, CIBERSORT<\/li>\n<li>\n    \u4e0b\u8f7d LM22.txt\u6570\u636e\u96c6 \u548c TCGA deg_fpkm.tsv \u6570\u636e\u6587\u4ef6<\/li>\n<\/ul>\n<p>install.packages(c(&#8220;ggplot2&#8221;, &#8220;ggpubr&#8221;, &#8220;reshape2&#8221;, &#8220;dplyr&#8221;, &#8220;CIBERSORT&#8221;))<\/p>\n<p><strong>\u6b65\u9aa4 2: \u8fd0\u884c CIBERSORT \u8fdb\u884c\u514d\u75ab\u7ec6\u80de\u7c7b\u578b\u5206\u6790<\/strong><\/p>\n<p>\u9996\u5148\uff0c\u6211\u4eec\u5c06\u4f7f\u7528 CIBERSORT \u5e93\u5bf9\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u8fdb\u884c\u514d\u75ab\u7ec6\u80de\u7c7b\u578b\u7684\u5206\u6790\u3002\u5177\u4f53\u6765\u8bf4\uff0c\u6211\u4eec\u5c06\u4ece LM22.txt \u548c TCGA deg_fpkm.tsv \u6587\u4ef6\u4e2d\u8bfb\u53d6\u57fa\u56e0\u8868\u8fbe\u6570\u636e\uff0c\u5e76\u4f7f\u7528 CIBERSORT \u51fd\u6570\u8ba1\u7b97\u51fa\u5404\u79cd\u514d\u75ab\u7ec6\u80de\u7c7b\u578b\u7684\u6bd4\u4f8b\u3002\u8bf7\u6309\u7167\u4ee5\u4e0b\u6b65\u9aa4\u8fdb\u884c\u64cd\u4f5c\uff1a<\/p>\n<ol>\n<li>\n  \u5c06 LM22.txt \u548c TCGA deg_fpkm.tsv \u6587\u4ef6\u653e\u5728\u5de5\u4f5c\u76ee\u5f55\u4e2d\u3002<\/li>\n<li>\n  \u8f93\u5165\u4ee5\u4e0b\u4ee3\u7801\uff0c\u5bfc\u5165\u6240\u9700\u7684\u5e93\uff1a<\/li>\n<\/ol>\n<p>library(CIBERSORT)<\/p>\n<ol>\n<li>\n  \u8f93\u5165\u4ee5\u4e0b\u4ee3\u7801\uff0c\u8bfb\u53d6\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u5e76\u8fd0\u884c CIBERSORT \u51fd\u6570\uff1a<\/li>\n<\/ol>\n<p>lm22.file &lt;- &#8220;LM22.txt&#8221;<\/p>\n<p>rawdata_file.file &lt;- &#8220;TCGA deg_fpkm.tsv&#8221;<\/p>\n<p>cibersort_file &lt;- &#8220;TCGA cibersort.txt&#8221;<\/p>\n<p>TCGA_TME.results &lt;- CIBERSORT(lm22.file, rawdata_file.file, perm = 50, QN = F)<\/p>\n<p>\u5176\u4e2d\uff0clm22.file \u548c rawdata_file.file \u5206\u522b\u4e3a LM22.txt \u548c TCGA deg_fpkm.tsv \u6587\u4ef6\u7684\u6587\u4ef6\u540d\uff0ccibersort_file \u4e3a\u8f93\u51fa\u6587\u4ef6\u540d\uff0cperm \u8868\u793a\u91cd\u590d\u8fd0\u884c\u7684\u6b21\u6570\uff0cQN \u8868\u793a\u662f\u5426\u8fdb\u884c\u91cf\u5316\u5f52\u4e00\u5316\u3002\u5c0f\u679c\u63d0\u9192\uff1a\u8fd0\u884c\u65f6\u95f4\u53ef\u80fd\u8f83\u957f\uff0c\u5177\u4f53\u53d6\u51b3\u4e8e\u6570\u636e\u96c6\u7684\u5927\u5c0f\u548c\u8ba1\u7b97\u673a\u7684\u6027\u80fd\u54e6\u3002<\/p>\n<ol>\n<li>\n  \u8f93\u5165\u4ee5\u4e0b\u4ee3\u7801\uff0c\u5c06 CIBERSORT \u8ba1\u7b97\u7ed3\u679c\u8f93\u51fa\u5230\u6587\u4ef6\u4e2d\uff1a<\/li>\n<\/ol>\n<p>write.csv(TCGA_TME.results, &#8220;TCGA_CIBERSORT_Results_fromRcode.csv&#8221;)<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"325\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30004-1.png?resize=640%2C325\" class=\"wp-image-30005\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30004-1.png?w=1884 1884w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30004-1.png?resize=300%2C152 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30004-1.png?resize=1024%2C520 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30004-1.png?resize=768%2C390 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30004-1.png?resize=1536%2C779 1536w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30004-1.png?resize=600%2C304 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30004-1.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><br \/>\n  \u63a5\u4e0b\u6765\uff0c\u5c0f\u679c\u5e26\u5927\u5bb6\u4e00\u8d77\u770b\u4e00\u4e0b\u6700\u540e\u751f\u6210\u7684\u7ed3\u679c\u6570\u636e\u662f\u4ec0\u4e48\u6837\u7684\u5427\uff01<\/p>\n<p>\u73b0\u5728\uff0c\u4f60\u5df2\u7ecf\u6210\u529f\u5b8c\u6210\u4e86\u514d\u75ab\u7ec6\u80de\u7c7b\u578b\u5206\u6790\u54e6\uff01\u600e\u4e48\u6837\uff0c\u662f\u4e0d\u662f\u5f88\u7b80\u5355\u5462\uff01<\/p>\n<p>\u600e\u4e48\u6837\uff0c\u4eca\u5929\u7684\u6559\u7a0b\u4f60\u5b66\u5e9f\u4e86\u561b\uff1f<strong>\u5c0f\u679c\u4e13\u5c5e\u4e91\u751f\u4fe1\u5e73\u53f0\uff1a<\/strong><a href=\"http:\/\/www.biocloudservice.com\/home.html\">\u4e91\u751f\u4fe1 \u00a0&#8211; \u5b66\u751f\u7269\u4fe1\u606f\u5b66 (biocloudservice.com)<\/a><\/p>\n<p>\u4e91\u751f\u4fe1\u5e73\u53f0\u4e5f\u6709\u514d\u75ab\u4e13\u7248\u7684\u5b66\u4e60\u6a21\u5757\u54e6\uff0c\u5feb\u6765\u627e\u5230\u4f60\u60f3\u5b66\u4e60\u7684\u4e13\u5c5e\u6a21\u5757\u5427\uff01<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"239\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-92.png?resize=640%2C239\" class=\"wp-image-30006\" alt=\"\u8868\u683c\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-92.png?w=895 895w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-92.png?resize=300%2C112 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-92.png?resize=768%2C287 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-92.png?resize=600%2C224 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u63ed\u5f00\u80bf\u7624\u514d\u75ab\u5206\u6790\u7684\u795e\u79d8\u9762\u7eb1\uff1a\u4f7f\u7528CIBERSORT\u5206\u6790\u4f60\u7684\u514d\u75ab\u7ec6\u80de\uff01 \u4eca\u5929\uff0c\u5c0f\u679c\u5c06\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u4e00\u4e2a\u57fa\u4e8e\u53cd\u5377\u79ef\u5206\u6790 [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30004"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=30004"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30004\/revisions"}],"predecessor-version":[{"id":30014,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30004\/revisions\/30014"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=30004"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=30004"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=30004"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}