{"id":301,"date":"2018-04-01T22:02:51","date_gmt":"2018-04-01T14:02:51","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=301"},"modified":"2018-04-03T10:32:13","modified_gmt":"2018-04-03T02:32:13","slug":"gsea%e5%91%bd%e4%bb%a4%e8%a1%8c","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=301","title":{"rendered":"GSEA\u547d\u4ee4\u884c"},"content":{"rendered":"<p>\u524d\u8fb9\u5df2\u7ecf\u8bf4\u5230MSigDB\u6570\u636e\u5e93\u7684entrez ID\u548csymble ID\u90fd\u662f\u4eba\u6e90\u7684\uff0c\u5176\u4ed6\u7269\u79cd\u8981\u60f3\u505aGSEA\u7684\u8bdd\uff0c\u5c31\u5fc5\u987b\u8981ID\u8f6c\u6362\uff0c\u505a\u6210\u5c5e\u4e8e\u81ea\u5df1\u7814\u7a76\u7269\u79cd\u7684\u6570\u636e\u5e93\uff0c\u8fd9\u4e00\u6b65\u662f\u5173\u952e\u3002\u60f3\u8981\u6839\u636e\u7b80\u5355\u7684Nr\u6ce8\u91ca\u6216\u5176\u4ed6\u6ce8\u91ca\u6765\u8f6c\u6362\u662f\u884c\u4e0d\u901a\u7684\uff0c\u6bd4\u5982\u6211\u7814\u7a76\u7684\u7269\u79cd\u4e3a\u786c\u9aa8\u9c7c\u7c7b\uff0cNr\u6ce8\u91ca\u7ed3\u679c\u5206\u503c\u6700\u9ad8\u7684\u524d20\u4e2a\u4e00\u822c\u4e5f\u90fd\u662f\u9c7c\u7c7b\uff0c\u5c31\u7b97\u6ce8\u91ca\u5230\u4e86\u4eba\u6e90\u7684\u57fa\u56e0\uff0c\u4e5f\u53ef\u80fd\u5b58\u5728\u7248\u672c\u4e0d\u5bf9\u7684\u95ee\u9898\u3002\u56e0\u6b64\u6211\u4eec\u8981\u77e5\u9053MSigDB\u6570\u636e\u5e93\u57fa\u56e0ID\u7684\u7248\u672c\uff0c\u7136\u540e\u4e0b\u8f7d\u5bf9\u5e94\u7684\u5168\u57fa\u56e0\u7ec4\u86cb\u767d\u5e8f\u5217\uff0c\u7136\u540e\u6bd4\u5bf9\u5361\u9608\u503c\uff0c\u505a\u6210\u81ea\u5df1\u7684\u6570\u636e\u5e93\u3002<\/p>\n<p>GSEA\u7684\u8fd0\u884c\u53ef\u4ee5\u754c\u9762\u64cd\u4f5c\u548c\u547d\u4ee4\u884c\u64cd\u4f5c\uff0c\u754c\u9762\u64cd\u4f5c\u6559\u7a0b\u5f88\u591a\u5c31\u4e0d\u591a\u505a\u8d58\u8ff0\uff0c\u5b83\u7684\u4e0d\u8db3\u4e4b\u5904\u9664\u4e86\u64cd\u4f5c\u7e41\u7410\u4e4b\u5916\uff0c\u91cc\u9762\u51e0\u4e2a\u8f83\u5927\u7684\u5e93\u9700\u8981\u7684\u5185\u5b58\u8f83\u9ad8\uff0c\u50cf\u6211\u76844G\u6e23\u6e23\u7535\u8111\uff0c\u597d\u51e0\u4e2a\u90fd\u8fd0\u884c\u5931\u8d25\uff0c\u4e0d\u5f97\u4e0d\u8f6c\u5230\u670d\u52a1\u5668\u4e0a\u8fd0\u884c\uff1b\u800c\u4e14\u754c\u9762\u4e5f\u4e0d\u80fd\u6279\u91cf\u8fd0\u884c\u3002<\/p>\n<pre>java -cp gsea-3.0.jar -Xmx10000m xtools.gsea.Gsea -res ma\/normalized_counts_all.gct -cls ma\/samples.cls#COS1_versus_COS0 -gmx ma\/ma.h.all.v6.1.symbols.gmt -collapse false -mode Max_probe -norm meandiv -nperm 1000 -permute gene_set -rnd_type no_balance -scoring_scheme weighted -rpt_label COS1vsCOS0_h -metric Ratio_of_Classes -sort real -order descending -create_gcts false -create_svgs false -include_only_symbols true -make_sets true -median false -num 100 -plot_top_x 20 -rnd_seed timestamp -save_rnd_lists false -set_max 2000 -set_min 5 -zip_report false -out multiple -gui false<\/pre>\n<p>-Xmx10000m:\u8bbe\u7f6e\u6700\u5927\u5185\u5b5810000\u5146\uff0c\u4e4b\u524d\u754c\u9762\u64cd\u4f5c\u5931\u8d25\u5c31\u56e0\u4e3a\u8fd9\u4e2a\u53c2\u6570<br \/>\n-res\uff1a\u8868\u8fbe\u91cf\u6587\u4ef6<br \/>\n-cls\uff1a\u6837\u672c\u4fe1\u606f<br \/>\n-gmx\uff1a\u6570\u636e\u5e93\u6587\u4ef6<br \/>\n-nperm\uff1aNumber of permutations<br \/>\n-rpt_label\uff1a\u8f93\u51fa\u6587\u4ef6\u7684\u524d\u7f00<br \/>\n-metric\uff1a\u6392\u5e8f\u7684\u65b9\u6cd5\uff0c\u5982\u679c\u6709\u91cd\u590d\uff0c\u53ef\u4ee5\u8003\u8651\u4f7f\u7528T-test\uff1b\u65e0\u91cd\u590d\uff0c\u53ef\u4ee5\u8003\u8651\u4f7f\u7528Ratio of calsses\uff08\u5dee\u5f02\u500d\u6570\uff09\u6216Diff of classes(\u5dee\u5f02\u7edd\u5bf9\u503c\uff09<br \/>\n-plot_top_x\uff1a\u9ed8\u8ba420\uff0c\u4ee3\u8868\u5bcc\u96c6\u5206\u6790\u6392\u540d\u6700\u9ad8\u768420\u4e2a\u901a\u8def<br \/>\n-set_max\uff1a\u901a\u8def\u57fa\u56e0\u7684\u6700\u5927\u6570\u91cf\uff0c\u9ed8\u8ba4500\uff0c\u4f46\u7531\u4e8e\u67d0\u4e9b\u901a\u8def\u57fa\u56e0\u6570\u5927\u4e8e500\uff0c\u5efa\u8bae\u63d0\u9ad8\u9608\u503c<br \/>\n-set_min\uff1a\u901a\u8def\u57fa\u56e0\u7684\u6700\u5c0f\u6570\u91cf\uff0c\u9ed8\u8ba415<br \/>\n-out\uff1a\u8f93\u51fa\u7684\u6587\u4ef6\u5939<br \/>\n\u5176\u4ed6\u53c2\u6570\u5747\u4e3a\u9ed8\u8ba4<\/p>\n<p>\u7248\u6743\u58f0\u660e\uff1a\u672c\u6587\u4e3a\u535a\u4e3b\u539f\u521b\u6587\u7ae0\uff0c\u672a\u7ecf\u535a\u4e3b\u5141\u8bb8\u4e0d\u5f97\u8f6c\u8f7d\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u524d\u8fb9\u5df2\u7ecf\u8bf4\u5230MSigDB\u6570\u636e\u5e93\u7684entrez ID\u548csymble ID\u90fd\u662f\u4eba\u6e90\u7684\uff0c\u5176\u4ed6\u7269\u79cd\u8981\u60f3\u505aGSEA\u7684\u8bdd\uff0c\u5c31\u5fc5\u987b\u8981ID\u8f6c\u6362\uff0c\u505a\u6210\u5c5e\u4e8e\u81ea\u5df1\u7814\u7a76\u7269\u79cd\u7684\u6570\u636e\u5e93\uff0c\u8fd9\u4e00\u6b65\u662f\u5173\u952e\u3002\u60f3\u8981\u6839\u636e\u7b80\u5355\u7684Nr\u6ce8\u91ca\u6216\u5176\u4ed6\u6ce8\u91ca\u6765\u8f6c\u6362\u662f\u884c\u4e0d\u901a\u7684\uff0c\u6bd4\u5982\u6211\u7814\u7a76\u7684\u7269\u79cd\u4e3a\u786c\u9aa8\u9c7c\u7c7b\uff0cNr\u6ce8\u91ca\u7ed3\u679c\u5206\u503c\u6700\u9ad8\u7684\u524d20\u4e2a\u4e00\u822c\u4e5f\u90fd\u662f\u9c7c\u7c7b\uff0c\u5c31\u7b97\u6ce8\u91ca\u5230\u4e86\u4eba\u6e90\u7684\u57fa\u56e0\uff0c\u4e5f\u53ef\u80fd\u5b58\u5728\u7248\u672c\u4e0d\u5bf9\u7684\u95ee\u9898\u3002\u56e0\u6b64\u6211\u4eec\u8981\u77e5\u9053MSigDB\u6570\u636e\u5e93\u57fa\u56e0ID\u7684\u7248\u672c\uff0c\u7136\u540e\u4e0b\u8f7d\u5bf9\u5e94\u7684\u5168\u57fa\u56e0\u7ec4\u86cb\u767d\u5e8f\u5217\uff0c\u7136\u540e\u6bd4\u5bf9\u5361\u9608\u503c\uff0c\u505a\u6210\u81ea\u5df1\u7684\u6570\u636e\u5e93\u3002 GSEA\u7684\u8fd0\u884c\u53ef\u4ee5\u754c\u9762\u64cd\u4f5c\u548c\u547d\u4ee4\u884c\u64cd\u4f5c\uff0c\u754c\u9762\u64cd\u4f5c\u6559\u7a0b\u5f88\u591a\u5c31\u4e0d\u591a\u505a\u8d58\u8ff0\uff0c\u5b83\u7684\u4e0d\u8db3\u4e4b\u5904\u9664\u4e86\u64cd\u4f5c\u7e41\u7410\u4e4b\u5916\uff0c\u91cc\u9762\u51e0\u4e2a\u8f83\u5927\u7684\u5e93\u9700\u8981\u7684\u5185\u5b58\u8f83\u9ad8\uff0c\u50cf\u6211\u76844G\u6e23\u6e23\u7535\u8111\uff0c\u597d\u51e0\u4e2a\u90fd\u8fd0\u884c\u5931\u8d25\uff0c\u4e0d\u5f97\u4e0d\u8f6c\u5230\u670d\u52a1\u5668\u4e0a\u8fd0\u884c\uff1b\u800c\u4e14\u754c\u9762\u4e5f\u4e0d\u80fd\u6279\u91cf\u8fd0\u884c\u3002 java -cp gsea-3.0.jar -Xmx10000m xtools.gsea.Gsea -res ma\/normalized_counts_all.gct -cls ma\/samples.cls#COS1_versus_COS0 -gmx ma\/ma.h.all.v6.1.symbols.gmt -collapse false -mode Max_probe -norm meandiv -nperm 1000 -permute gene_set -rnd_type no_balance -scoring_scheme weighted -rpt_label COS1vsCOS0_h -metric Ratio_of_Classes -sort real -order descending -create_gcts false -create_svgs false -include_only_symbols true -make_sets true -median false -num 100 -plot_top_x 20 -rnd_seed timestamp -save_rnd_lists false [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/301"}],"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=301"}],"version-history":[{"count":9,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/301\/revisions"}],"predecessor-version":[{"id":314,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/301\/revisions\/314"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=301"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=301"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=301"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}