{"id":242,"date":"2009-08-19T08:57:14","date_gmt":"2009-08-19T08:57:14","guid":{"rendered":"http:\/\/tw.newtonstudio.com\/?p=242"},"modified":"2009-08-19T08:57:14","modified_gmt":"2009-08-19T08:57:14","slug":"rdata-analysis","status":"publish","type":"post","link":"http:\/\/tw.newtonstudio.com\/?p=242","title":{"rendered":"[R]Data Analysis"},"content":{"rendered":"<p>Class Comparison: \u6bd4\u8f03\u4e0d\u540cClass\u7684\u985e\u5225, \u5c6c\u6027<\/p>\n<p>Class Discovery: \u5f9e\u4e00\u7fa4Data\u4e2d\u53bb\u6b78\u985e, \u76f8\u4f3c\u6027<\/p>\n<p>Class Prediction: \u6709\u65b0\u7684data, \u80fd\u4e0d\u80fd\u7528\u4f86\u6b78\u985e\u65bc\u73fe\u6709\u7684Class<\/p>\n<hr \/>\n<p><strong>Class Comparison<\/strong><\/p>\n<p>\u627e\u51fa\u986f\u8457\u5dee\u7570\u7684.<\/p>\n<p>\u4e0d\u8003\u616e\u57fa\u56e0\u8207\u57fa\u56e0\u7684Interactions.<\/p>\n<p>\u7528FoldChange(FC) = Expression of Experriment al Sample \/ Expresssion of Reference Sample<\/p>\n<p>\u53ef\u7528Scatter plots \u53ca MA-plots Visualized, \u4f46Fold-Change\u6c92\u8fa6\u6cd5\u627e\u51fa\u986f\u8457\u5dee\u7570, \u4e0d\u5177\u6709\u7d71\u8a08\u610f\u7fa9,\u4f46\u9084\u662f\u5f88\u591a\u4eba\u559c\u6b61\u4f7f\u7528, why? \u56e0\u70ba\u7d71\u8a08\u4e0a\u9700\u8981\u5927\u91cf\u7684SAMPLE, \u800c\u4e00\u822c\u5be6\u9a57\u6c92\u6709\u90a3\u9ebc\u591a\u7684sample, \u53ea\u80fd\u7528Fold Change \u4f86\u8868\u793a.<\/p>\n<p>P-value: \u6a5f\u7387\u7684\u6982\u5ff5. \u5728\u6b63\u5e38\u60c5\u6cc1\u4e0b, \u6211\u770b\u5230\u9019\u6a23\u7684CASE\u7684\u6a5f\u7387\u5230\u5e95\u6709\u591a\u5c11? \u4f8b\u5982: \u5728\u5927\u5bb6\u90fd\u8cb7\u6a02\u900f\u7684\u60c5\u6cc1\u4e0b. p-value\u8d8a\u5c0f\u8d8a\u597d, \u8868\u793a\u8d8a\u986f\u8457. alpha-value\u662f\u81e8\u754c\u503c, \u82e5p-value\u5c0f\u65bcalpha-value, \u5247\u6709\u986f\u8457. \u6240\u4ee5\u4e00\u822c\u4e0a\u7fd2\u6163\u628aalpha-value\u8a2d\u5f97\u6bd4\u8f03\u5c0f.<\/p>\n<p>\u5206\u6790\u4e00\u822c\u7684 Microarray data\u65b9\u6cd5:<\/p>\n<p><strong>Parametric\u00a0 Hypothesis Testing (\u6709\u5e38\u614b\u5206\u5e03)<br \/>\n<\/strong><\/p>\n<ul>\n<li><em>Paired Data<\/em> :z-test, t-test<\/li>\n<li><em>Unpaired Data<\/em> :two-sample, t-test<\/li>\n<li><em>Complex Data (more than 2 groups)<\/em> :One-way Analysis of Variance(ANOVA)<\/li>\n<\/ul>\n<p><strong>Non-Parametric Hypothesis Testing (\u4e0d\u5408\u5e38\u614b\u5206\u5e03)<br \/>\n<\/strong><\/p>\n<ul>\n<li><em>Paired data<\/em>: Sign test, Wilcoxon signed-rank test<\/li>\n<li><em>Unpaired Data<\/em> :Wilcoxon rank-sum test, (Mann-Whitney U test).<\/li>\n<li><em>Complex Data<\/em> :Kruskal-Wallis test<\/li>\n<\/ul>\n<p>\u5982\u4f55\u77e5\u9053\u6709\u7121\u5e38\u614b\u5206\u5e03? \u7528 QQplot, Shapiro&#8230;.<\/p>\n<p>Parametric Statistics<\/p>\n<p><strong>Paired Data: \u5982\u5316\u7642\u524d, \u5316\u7642\u5f8c\u7684\u6bd4\u8f03, \u5403\u85e5\u524d, \u5403\u85e5\u5f8c.<\/strong><\/p>\n<blockquote><p>t.test(x,y,paired =TRUE, alternative = c(&#8220;two.sided&#8221;, &#8220;less&#8221;, &#8220;greater&#8221;))<\/p><\/blockquote>\n<p>\u4e00\u5b9a\u8981\u5148\u5c0d\u597d\u5169\u7d44\u6578\u64da, \u7136\u5f8c\u53c3\u6578paired = TRUE\u8981\u5beb.<\/p>\n<p><strong>Unpaired Data: sample\u4f86\u81ea\u4e0d\u540c\u7684\u5730\u65b9<\/strong><\/p>\n<p>\u5148\u7528var.test \u6e2c\u8a66p-value\u662f\u5426\u6709\u986f\u8457, \u82e5\u8d8a\u5927\u5c31\u8d8a\u4e0d\u986f\u8457.<\/p>\n<blockquote><p>if(sigmaa = sigmab),<\/p>\n<p>var.test(x,y, var.equal = TRUE)<\/p>\n<p>if(sigmaa != sigmab),<\/p>\n<p>var.test(x,y, var.equal=FALSE)<\/p><\/blockquote>\n<p><strong>Complex Data: (Using ANOVA)<\/strong><\/p>\n<p>Example: All dataset<\/p>\n<p>y = drop(exprs(eset[1,]))<\/p>\n<p>out = lm(y~factor(c1)) \/\/lm \u8b8a\u65b9\u5206\u6790<\/p>\n<p>anova(out)<\/p>\n<p><strong>Non-Parametric Statistics<\/strong><\/p>\n<p>\u57fa\u672c\u4e0amicroarray \u662f\u5f88\u96dc\u4e82\u7684, \u4e0d\u9069\u5408\u7528\u4ee5\u4e0a\u7684parametric \u65b9\u5f0f, \u6545\u4f7f\u7528\u9019\u7a2e\u7d71\u8a08\u65b9\u5f0f.<\/p>\n<p><strong>Paired<\/strong><\/p>\n<p>wilcox.test(x, y, paired= TRUE, alternative = c(&#8220;two.sided&#8221;, &#8220;less&#8221;, &#8220;greater&#8221;))<\/p>\n<p><strong>Unpaired<\/strong><\/p>\n<p>wilcox.test(x, y,  alternative = c(&#8220;two.sided&#8221;, &#8220;less&#8221;, &#8220;greater&#8221;))<\/p>\n<p><strong>Anova<\/strong><\/p>\n<p>\u53c3\u8003\u6295\u5f71\u7247<\/p>\n<hr \/>\n<p><strong>Permutation Tests<\/strong><\/p>\n<p>What&#8217;s this? \u6392\u5217. \u96a8\u6a5f\u6392\u5217.<\/p>\n<p>\u6bd4\u5982\u8aaa, \u670910\u500b\u57fa\u56e0, \u6bcf\u500b\u4f5c2\u6b21 \u5c31\u670920\u6b21. \u628a10\u500b\u7d50\u679c\u4f5c\u96a8\u6a5f\u6392\u5217, \u5206\u524d\u4e94\u500b, \u5f8c\u4e94\u500b, \u8a08\u7b97\u6bcf\u500b\u51fa\u73fe\u7684\u6a5f\u7387.<\/p>\n<p>\u6703\u5f62\u6210\u4e00\u500b\u5e38\u614b\u5206\u5e03. Steps\u53ef\u53c3\u8003\u6559\u5b78\u6295\u5f71\u7247.<\/p>\n<p>\u8cc7\u6599\u6578\u592a\u5c11\u7684\u6642\u5019\u4e0d\u9069\u5408\u7528Permutation test, \u61c9\u8a72\u4f7f\u7528&#8221;Bootstrap&#8221;.<\/p>\n<p><strong>\u7528R\u4f5cpermutation test:<\/strong><\/p>\n<p>&#8220;multtest&#8221; package<\/p>\n<p>mt.sample.teststat: to compute permuted statistcs<\/p>\n<p>mt.sample.rawp: to compute the p-values<\/p>\n<p><strong>Note: &#8220;test&#8221; includes:<\/strong><\/p>\n<p>t, t.equalvar, pairt, wilcoxon, f<\/p>\n<p><strong>Bootstrap<\/strong><\/p>\n<p>boot.out = boot(englife, function(x, id) {median(x[id])}, 1000}<\/p>\n<p>how many bootstraps ? rule of thumb: 100 times. \u53ef\u4ee5\u518d\u8a66\u8a66\u770b1000\u6b21, 10000\u6b21.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Class Comparison: \u6bd4\u8f03\u4e0d\u540cClass\u7684\u985e\u5225, \u5c6c\u6027 Class Discovery: \u5f9e\u4e00\u7fa4 [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[85],"tags":[],"class_list":["post-242","post","type-post","status-publish","format-standard","hentry","category-r"],"_links":{"self":[{"href":"http:\/\/tw.newtonstudio.com\/index.php?rest_route=\/wp\/v2\/posts\/242","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/tw.newtonstudio.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/tw.newtonstudio.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/tw.newtonstudio.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/tw.newtonstudio.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=242"}],"version-history":[{"count":8,"href":"http:\/\/tw.newtonstudio.com\/index.php?rest_route=\/wp\/v2\/posts\/242\/revisions"}],"predecessor-version":[{"id":250,"href":"http:\/\/tw.newtonstudio.com\/index.php?rest_route=\/wp\/v2\/posts\/242\/revisions\/250"}],"wp:attachment":[{"href":"http:\/\/tw.newtonstudio.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=242"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/tw.newtonstudio.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=242"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/tw.newtonstudio.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=242"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}