{"id":282,"date":"2009-08-24T05:42:37","date_gmt":"2009-08-24T05:42:37","guid":{"rendered":"http:\/\/tw.newtonstudio.com\/?p=282"},"modified":"2009-08-24T08:16:59","modified_gmt":"2009-08-24T08:16:59","slug":"microarray-preprocessing","status":"publish","type":"post","link":"http:\/\/tw.newtonstudio.com\/?p=282","title":{"rendered":"[R]MicroArray Preprocessing"},"content":{"rendered":"

Preprocessing includes<\/strong>
\n\u2013 Image analysis and data import
\n\u2013 Background adjustment
\n\u2013 Normalization
\n\u2013 Summarization (for Affymetrix)
\n\u2013 Quality assessment<\/p>\n

Practise Data:<\/strong><\/p>\n

\"\"<\/a><\/p>\n

\u4f7f\u7528limmaGUI\u532f\u5165two-channel microarray data<\/p>\n

\u53c3\u8003: http:\/\/bioinf.wehi.edu.au\/limmaGUI\/<\/strong><\/p>\n

A. \u4e0b\u8f09 Swirl Zebrafish\u8cc7\u6599<\/strong><\/p>\n

http:\/\/bioinf.wehi.edu.au\/limmaGUI\/Swirl\/swirl.zip<\/p>\n

B. \u5b89\u88dd Bioconductor<\/strong><\/p>\n

> source(“http:\/\/bioconductor.org\/biocLite.R”)<\/p>\n

> biocLite()<\/p>\n

C. \u5b89\u88dd\u4ee5\u4e0bpackages: convert, limma, arrayQuality, marray, mclust, hexbin, limmaGUI, sma, tkrplot, R2HTML, statmod<\/strong><\/p>\n

    \n
  1. \u7a0b\u5f0f\u5957\u4ef6 > \u9078\u64c7\u5b58\u653e\u8655 > CRAN, CRAN(extra), BioC software<\/li>\n
  2. \u7a0b\u5f0f\u5957\u4ef6 > \u5b89\u88dd\u7a0b\u5f0f\u5957\u4ef6 (\u6216\u7528install.packages(“convert”)<\/li>\n<\/ol>\n

    \u5229\u7528affylmGUI\u532f\u5165two-channel microarray data:<\/p>\n

    \u6e96\u5099\u52d5\u4f5c:<\/p>\n

    A \u5b89\u88ddestrogen package\u4ee5\u53d6\u5f97estrogene dataset:<\/strong><\/p>\n

      \n
    1. \u7a0b\u5f0f\u5957\u4ef6 > \u9078\u64c7\u5b58\u653e\u8655 > BioC experiment<\/li>\n
    2. \u7a0b\u5f0f\u5957\u4ef6 > \u5b89\u88dd\u7a0b\u5f0f\u5957\u4ef6<\/li>\n<\/ol>\n

      B. \u5b89\u88ddaffylmGUI packages:<\/strong><\/p>\n

        \n
      1. \u7a0b\u5f0f\u5957\u4ef6 > \u9078\u64c7\u5b58\u653e\u8655 > BioC Software<\/li>\n
      2. \u7a0b\u5f0f\u5957\u4ef6 > \u5b89\u88dd\u7a0b\u5f0f\u5957\u4ef6<\/li>\n<\/ol>\n

        Normalization<\/strong><\/p>\n

        To identify and remove systematic sources of variation in the measured fluorescence intensities, such as<\/p>\n

        – different labelling efficiencies of the dyes;<\/p>\n

        – different scanning parameters;<\/p>\n

        – sector\/print-tip, spatial, or plate effects, etc.<\/p>\n

        \u4e0d\u8981\u505a\u904e\u591a\u7684normalization, \u56e0\u70ba\u53ef\u80fd\u628a\u539f\u672c\u662fsignal\u7684data\u5f04\u4e0d\u898b.<\/p>\n

        Self-self hybridization: \u53bb\u63a2\u8a0edye\u7684\u7cfb\u7d71\u6027\u8aa4\u5dee\u7684\u5178\u578b\u4f8b\u5b50; \u4f7f\u7528\u76f8\u540c\u7684sample, \u4e0d\u540c\u7684\u67d3\u5291, \u53bb\u505a\u67d3\u8272\u5c31\u53ef\u4ee5\u77e5\u9053\u4e0d\u540c\u67d3\u5291\u7684\u5dee\u7570\u6027, \u7406\u8ad6\u4e0a\u5448\u73fe\u7684pattern\u61c9\u8a72\u662f\u5982\u4e0b\u5de6\u5716, \u4f46\u5be6\u969b\u4e0a\u6703\u662f\u9577\u5f97\u50cf\u53f3\u5716\u7684:<\/p>\n

        \"\"<\/a>\"\"<\/a><\/p>\n

        \u6240\u4ee5\u5f9e\u4ee5\u4e0a\u7684\u4f8b\u5b50\u4f86\u770b, \u77ef\u6b63(Normalization)\u7684\u52d5\u4f5c\u8b8a\u5f97\u5f88\u91cd\u8981.<\/p>\n

        \u53ef\u4ee5\u7528: Within-Array Normalization.<\/p>\n

        \u5be6\u4f5c:<\/p>\n

        \u4f7f\u7528limmaGUI\u4f86\u4f5cNormalization:<\/p>\n

        Normalization > Select Within-Array Normalization<\/p>\n","protected":false},"excerpt":{"rendered":"

        Preprocessing includes \u2013 Image analysis and data import […]<\/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-282","post","type-post","status-publish","format-standard","hentry","category-r"],"_links":{"self":[{"href":"http:\/\/tw.newtonstudio.com\/index.php?rest_route=\/wp\/v2\/posts\/282","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=282"}],"version-history":[{"count":10,"href":"http:\/\/tw.newtonstudio.com\/index.php?rest_route=\/wp\/v2\/posts\/282\/revisions"}],"predecessor-version":[{"id":285,"href":"http:\/\/tw.newtonstudio.com\/index.php?rest_route=\/wp\/v2\/posts\/282\/revisions\/285"}],"wp:attachment":[{"href":"http:\/\/tw.newtonstudio.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=282"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/tw.newtonstudio.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=282"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/tw.newtonstudio.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=282"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}