{"id":2499,"date":"2017-09-24T17:19:16","date_gmt":"2017-09-24T09:19:16","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2499"},"modified":"2017-09-24T17:19:17","modified_gmt":"2017-09-24T09:19:17","slug":"%e4%bd%bf%e7%94%a8samr%e5%af%b9%e8%9b%8b%e7%99%bd%e7%bb%84%e6%95%b0%e6%8d%ae%e8%a1%a8%e8%be%be%e9%87%8f%e8%bf%9b%e8%a1%8c%e5%b7%ae%e5%bc%82%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2499","title":{"rendered":"\u4f7f\u7528SAMR\u5bf9\u86cb\u767d\u7ec4\u6570\u636e\u8868\u8fbe\u91cf\u8fdb\u884c\u5dee\u5f02\u5206\u6790"},"content":{"rendered":"

1. SAMR\u7b80\u4ecb<\/h1>\n

SAM\uff08Significance Analysis of Microarrays\uff09\u5728\u57fa\u56e0\u82af\u7247\u6570\u636e\u65f6\u4ee3\u4e2d\u88ab\u5f00\u53d1\u51fa\u6765\u8fdb\u884c\u57fa\u56e0\u8868\u8fbe\u91cf\u5dee\u5f02\u5206\u6790\u3002\u8be5\u7b97\u6cd5\u4e5f\u80fd\u7528\u4e8e\u8fdb\u884cRNA-Seq\u6570\u636e\u7684\u57fa\u56e0\u8868\u8fbe\u91cf\u5dee\u5f02\u5206\u6790\uff0c\u4f46\u8c8c\u4f3c\u8f83\u5c11\u4eba\u4f1a\u7528\u5b83\u8fdb\u884cRNA-Seq\u6570\u636e\u5206\u6790\u3002<\/p>\n

\u6700\u8fd1\u5728\u4e00\u7bc7\u5bf9\u86cb\u767d\u7ec4\u6570\u636e\u5dee\u5f02\u5206\u6790\u8f6f\u4ef6\u8fdb\u884c\u6bd4\u8f83\u7684\u6587\u7ae0\u4e2d\uff0cSAM\u7ed3\u679c\u8868\u73b0\u6700\u4f18\u3002\u672c\u6587\u5bf9\u57fa\u4e8eR\u8f6f\u4ef6\u7684SAM\u7b97\u6cd5\u8f6f\u4ef6SAMR\u7684\u4f7f\u7528\u8fdb\u884c\u7b80\u5355\u8bb2\u8ff0\u3002<\/p>\n

2. SAMR\u8f6f\u4ef6\u7684\u5b89\u88c5\u548c\u542f\u52a8<\/h1>\n

\u6253\u5f00R\u8f6f\u4ef6\uff0c\u8f93\u5165\u5982\u4e0b\u547d\u4ee4\u5b89\u88c5SAMR\u76f8\u5173\u7684\u5305\uff1a<\/p>\n

\r\n$ R\r\n> install.packages(c(\"samr\", \"matrixStats\", \"GSA\", \"shiny\", \"openxlsx\"))\r\n> source(\"http:\/\/bioconductor.org\/biocLite.R\")\r\n> biocLite(\"impute\")\r\n<\/pre>\n
\u8981\u6ce8\u610f\u7684\u662f\uff0c\u5bf9openxlsx\u5305\u7684\u5b89\u88c5\u53ef\u80fd\u4f1a\u5931\u8d25\uff08\u6211\u4f7f\u7528\u7684\u662fR-3.2.0\u7248\u672c\uff09\uff0c\u5219\u5728\u4e0a\u8ff0\u547d\u4ee4\u4e2d\u53bb\u9664\u5bf9openxlsx\u7684\u5b89\u88c5\uff0c\u9009\u62e9\u624b\u52a8\u4e0b\u8f7d\u5e76\u5b89\u88c5\u8001\u7248\u672c\u7684openxlsx\u5305\uff1a<\/p>\n
\r\n$ wget https:\/\/cran.r-project.org\/src\/contrib\/Archive\/openxlsx\/openxlsx_2.4.0.tar.gz\r\n$ R CMD INSTALL openxlsx_2.4.0.tar.gz\r\n<\/pre>\n
\u542f\u52a8SAMR\u8f6f\u4ef6\uff1a<\/p>\n
\r\n$ R\r\n> library(shiny)\r\n> runGitHub(\"SAM\", \"MikeJSeo\")\r\n<\/pre>\n
\u542f\u52a8SAMR\u8f6f\u4ef6\uff0c\u5219\u4f1a\u81ea\u52a8\u6253\u5f00CentOS 6.8\u7cfb\u7edf\u81ea\u5e26\u7684\u706b\u72d0\u6d4f\u89c8\u5668\uff0c\u8fdb\u5165\u8f6f\u4ef6\u7684\u7f51\u9875\u754c\u9762\u3002<\/p>\n
3. SARM\u8f6f\u4ef6\u4f7f\u7528<\/h1>\n
3.1 \u8f93\u5165\u6587\u4ef6\u51c6\u5907<\/h2>\n
\u8f6f\u4ef6\u7684\u8f93\u5165\u6587\u4ef6\u5fc5\u987b\u662fxlsx\u683c\u5f0f\u7684EXCEL\u6587\u4ef6\u3002\u8fdb\u884c\u86cb\u767d\u7ec4\u8868\u8fbe\u91cf\u6570\u636e\u8fdb\u884c\u5206\u6790\uff0c\u5176\u6587\u4ef6\u5185\u5bb9\u8981\u6c42\u5982\u4e0b\uff1a<\/p>\n
\r\n1. \u7b2c\u4e00\u5217\u662f\u57fa\u56e0Name\uff0c\u7b2c\u4e8c\u5217\u662f\u57fa\u56e0ID\uff0c\u6bcf\u4e2a\u57fa\u56e0ID\u5e94\u8be5\u72ec\u4e00\u65e0\u4e8c\u3002\r\n2. \u7b2c\u4e00\u884c\u8868\u793a\u6837\u54c1\u540d\uff0c\u7b2c\u4e00\u884c\u7b2c\u4e00\u5217\u548c\u7b2c\u4e00\u884c\u7b2c\u4e8c\u5217\u662f\u7a7a\u7740\u7684\uff0c\u4ece\u7b2c\u4e09\u5217\u5f00\u59cb\u8868\u793a\u6837\u54c1\u540d\uff0c\u4e14\u6837\u54c1\u540d\u4ec5\u80fd\u662f\u6570\u5b571\u62162\uff0c\u4ee3\u8868\u4e24\u4e2a\u4e0d\u540c\u7684\u6837\u54c1\u3002\u90fd\u4f7f\u7528\u6570\u5b571\u8868\u793a\u6837\u54c11\u7684\u591a\u4e2a\u91cd\u590d\uff0c\u90fd\u4f7f\u7528\u6570\u5b572\u8868\u793a\u6837\u54c12\u7684\u591a\u4e2a\u91cd\u590d\u3002\u867d\u7136SARM\u80fd\u5206\u6790\u591a\u4e2a\u6837\u54c1\u7684\u6570\u636e\uff0c\u4f46\u662f\u5176\u7ed3\u679c\u683c\u5f0f\u4e0d\u597d\uff0c\u4e00\u822c\u662f\u8fdb\u884c\u4e24\u4e24\u6bd4\u8f83\u3002\r\n3. \u82e5\u6709\u6570\u636e\u7f3a\u5931\uff0c\u5219\u67d0\u884c\u67d0\u5217\u4e0d\u586b\u5165\u6570\u636e\uff0c\u6216\u586b\u5165\u975e\u6570\u5b57\uff08\u63a8\u8350 NA\uff09\u4ee3\u66ff\u3002\r\n4. \u82e5\u6709\u591a\u7ec4\u6837\u54c1\u8fdb\u884c\u6bd4\u8f83\uff0c\u5219\u9700\u8981\u51c6\u5907\u591a\u4e2aexcel\u6587\u4ef6\uff0c\u800c\u4e0d\u662f\u4e00\u4e2aexcel\u6587\u4ef6\uff0c\u591a\u4e2asheet\u3002\r\n<\/pre>\n
3.2 \u5728\u7f51\u9875\u4e2d\u8fdb\u884cSAMR\u64cd\u4f5c<\/h2>\n
\u6309\u5982\u4e0b\u6b65\u9aa4\u8fdb\u884c\u64cd\u4f5c\uff1a<\/p>\n
\r\n1. \u70b9\u51fb Browse\uff0c\u9009\u4e2d\u76ee\u6807excel\u6587\u4ef6\u3002\r\n2. \u5728 Minimum fold change \u4e00\u680f\u4e2d\u586b\u5199\u4e00\u4e2a\u6700\u5c0f\u7684\u5dee\u5f02\u500d\u6570\u503c\uff0c\u6bd4\u5982 1.5 \u6216 2 \u7b49\u3002\r\n3. \u5728 Data type \u4e00\u680f\u9009\u62e9\u9ed8\u8ba4\u7684 Array \u3002\r\n4. \u5728 Response Type \u4e00\u680f\u9009\u62e9 Two class unpaired\u3002\u8fd9\u4e2a\u9009\u62e9\u9879\u6709\u5f88\u591a\uff0c\u4e0e\u8f93\u5165\u6587\u4ef6\u7684\u6570\u636e\u683c\u5f0f\u76f8\u5173\uff0c\u6211\u4eec\u662f\u5bf9\u4e24\u4e2a\u6837\u54c1\u8fdb\u884c\u6bd4\u8f83\uff0c\u6545\u9009\u62e9\u6b64\u9009\u9879\u3002\u8f93\u5165\u6587\u4ef6\u7b2c\u4e00\u5217\u4e0d\u662f1\u548c2\uff0c\u662f\u4e0d\u540c\u7684\u6570\u503c\uff08\u6bd4\u5982\u8840\u538b\uff09\uff0c\u6b64\u5904\u5219\u9009\u62e9Quantitative\u3002\r\n5. \u5728 Analysis Type \u4e00\u680f\u9009\u62e9\u9ed8\u8ba4\u7684 Standard \u5373\u53ef\u3002\r\n6. \u5728 Test Statistic \u4e00\u680f\u9009\u62e9\u9ed8\u8ba4\u7684 T-statistic \u5373\u53ef\u3002\r\n7. \u5728 Median Center the arrarys \u4e00\u680f\u9009\u62e9 Yes\u3002\u9009\u62e9Yes\u8868\u793a\u8f6f\u4ef6\u4f1a\u6839\u636e\u4e2d\u4f4d\u6570\u6765\u5bf9\u6570\u636e\u8fdb\u884c\u6807\u51c6\u5316\uff0c\u5373\u8ba9\u6bcf\u4e00\u5217\u7684\u4e2d\u4f4d\u6570\u90fd\u53d8\u6210\u96f6\u3002\u8fd9\u6837\u6bcf\u4e2a\u6837\u54c1\u7684\u6570\u636e\u90fd\u5177\u6709\u76f8\u540c\u7684\u4e2d\u4f4d\u6570\uff0c\u76f8\u5f53\u4e8e\u8fdb\u884c\u4e86\u6837\u54c1\u95f4\u7684\u6807\u51c6\u5316\u3002\u8f6f\u4ef6\u63a8\u8350\u5728\u8f93\u5165\u6570\u636e\u4e4b\u524d\u8fdb\u884c\u6807\u51c6\u5316\uff08\u4e0d\u5982TMM\u7b97\u6cd5\u8fdb\u884c\u6807\u51c6\u5316\uff09\uff0c\u82e5\u8f93\u5165\u7684\u6570\u636e\u662f\u6807\u51c6\u5316\u540e\u7684\u6570\u636e\uff0c\u5219\u6b64\u680f\u9009\u62e9\u9ed8\u8ba4\u7684 No\u3002\r\n8. \u5176\u5b83\u53c2\u6570\u9009\u62e9\u4e00\u822c\u60c5\u51b5\u4e0b\u9009\u62e9\u9ed8\u8ba4\u7684\u5373\u53ef\u3002\r\n9. \u70b9\u51fb\u5de6\u4e0a\u89d2\u7684 Run \u6309\u94ae\u8fdb\u884c\u5206\u6790\uff0c\u5206\u5f00\u5f97\u5230\u7ed3\u679c\uff0c\u5728\u53f3\u8fb9\u5404\u4e2a\u6807\u7b7e\u680f\u8fdb\u884c\u67e5\u770b\u7ed3\u679c\u3002\r\n10. \u5728 Delta Table \u9875\u9762\u4e0b\u67e5\u770b Median FDR \u503c\uff0c\u4ece\u4e0a\u5f80\u4e0b\u627e\u5230\u8be5\u503c\u53d8\u4e3a0.05\u65f6\u7684delta\u503c\uff0c\u518d\u5728\u5de6\u4fa7 Delta \u4e00\u680f\u9009\u62e9 manually Enter Delta, \u7136\u540e\u518d\u5728 Delta value \u4e00\u680f\u586b\u5165\u8be5\u503c\uff0c\u518d\u8fdb\u884c\u8ba1\u7b97\u3002\u7136\u540e\u70b9\u51fbCurrent Settings\u6807\u7b7e\u9875\uff0c\u770b\u5176False Discovery Rate\u7684\u503c\uff0c\u624b\u52a8\u8c03\u6574 Delta \u503c\uff0c\u76f4\u5230 FDR \u503c\u6700\u63a5\u8fd1\u5e76\u4f4e\u4e8e 0.05 \u4e3a\u6b62\u3002Delta\u503c\u8d8a\u5927\uff0cFDR\u503c\u8d8a\u5c0f\u3002\r\n11. \u5728 Paste the filepath to save the output \u4e00\u680f\u586b\u5165\u9700\u8981\u8f93\u51fa\u7684\u6587\u4ef6\u5939\u8def\u5f84\uff0c\u8be5\u8def\u5f84\u4e00\u5b9a\u8981\u5b58\u5728\uff0c\u5728\u5176\u4e0b\u4e00\u680f\u586b\u5165\u8f93\u51fa\u6587\u4ef6\u7684\u524d\u7f00\uff0c\u6bd4\u5982 out \u3002 \u5728\u70b9\u51fb Save\uff0c\u7136\u540e\u4f1a\u8f93\u51fa\u7ed3\u679c\u6587\u4ef6 out.xlsx\uff0c\u8be5excel\u6587\u4ef6\u6709\u591a\u4e2asheet\u5206\u522b\u591a\u4e2a\u6807\u7b7e\u9875\u4e2d\u7684\u7ed3\u679c\u3002\r\n<\/pre>\n
4. SARM \u8f6f\u4ef6\u7b97\u6cd5\u548c\u539f\u7406<\/h1>\n
\u8fd9\u4e2a\u6bd4\u8f83\u590d\u6742\uff0c\u6211\u4e5f\u4e0d\u600e\u4e48\u641e\u61c2\uff0c\u5305\u62ec\u7ed3\u679c\u4e2d\u4e00\u4e9bDelta, Score(d), q-value, FDR, localfdr\u7b49\uff0c\u6709\u70b9\u7cca\u6d82\u3002\u7b49\u4ee5\u540e\u6709\u65f6\u95f4\u641e\u66f4\u660e\u767d\u4e86\uff0c\u518d\u6dfb\u52a0\u89e3\u91ca\u3002<\/p>\n
\r\nDelta value\uff1a\r\nScore(d)\uff1aT\u68c0\u9a8c\u7684\u7684d\u503c\uff0c\u7531 Numerator(r) \/ Denominator(s+s0) \u5f97\u5230\u3002\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"
1. SAMR\u7b80\u4ecb SAM\uff08Significance Analysis of M … \u7ee7\u7eed\u9605\u8bfb →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[1],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2499"}],"collection":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=2499"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2499\/revisions"}],"predecessor-version":[{"id":2500,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2499\/revisions\/2500"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2499"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2499"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2499"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}