{"id":480,"date":"2006-12-10T10:18:06","date_gmt":"2006-12-10T08:18:06","guid":{"rendered":"http:\/\/www.wjst.de\/blog\/2006\/12\/10\/how-to-detect-your-own-cnvs\/"},"modified":"2006-12-10T10:18:06","modified_gmt":"2006-12-10T08:18:06","slug":"how-to-detect-your-own-cnvs","status":"publish","type":"post","link":"https:\/\/www.wjst.de\/blog\/sciencesurf\/2006\/12\/how-to-detect-your-own-cnvs\/","title":{"rendered":"How to detect your own CNVs"},"content":{"rendered":"<p>How to detect copy number variation (CNV) in your own genotype chip data, can be found in a <a href=\"http:\/\/www.genome.org\/cgi\/content\/full\/16\/12\/1575\">companion paper<\/a> of the recent <a href=\"https:\/\/www.wjst.de\/blog\/2006\/11\/24\/nothing-makes-sense-except-in-the-light-of-a-hypothese\/\">Nature publication<\/a>.<br \/>\nIn the previous Nature paper the authors explained their algorithm to be based on k-means and PAM (partitioning around medoid) clustering, but it seems quite different. They call genotypes with DM (which seems to be already obsolete by the BRLMM, see a comparison at <a href=\"http:\/\/www.broad.mit.edu\/gen_analysis\/genotyping\/brlmm_affy_ncrr.html\">Broad<\/a> and the <a href=\"http:\/\/www.affymetrix.com\/support\/technical\/whitepapers\/brlmm_whitepaper.pdf\">AFFX whitepaper<\/a>), then adjust heterocygote ratios by Gaussian mixture clustering, normalize and reduce noise before! merging NspI and StyI arrays. The software is at <a href=\"http:\/\/www2.genome.rcast.u-tokyo.ac.jp\/CNV\/\">Genome Science, Tokyo<\/a>. Yea, yea.<\/p>\n\n<p>&nbsp;<\/p>\n<div class=\"bottom-note\">\n  <span class=\"mod1\">CC-BY-NC Science Surf , accessed 09.04.2026<\/span>\n <\/div>","protected":false},"excerpt":{"rendered":"<p>How to detect copy number variation (CNV) in your own genotype chip data, can be found in a companion paper of the recent Nature publication. In the previous Nature paper the authors explained their algorithm to be based on k-means and PAM (partitioning around medoid) clustering, but it seems quite different. They call genotypes with &hellip; <a href=\"https:\/\/www.wjst.de\/blog\/sciencesurf\/2006\/12\/how-to-detect-your-own-cnvs\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">How to detect your own CNVs<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[2,9],"tags":[270,2949,2945,402,291,405,410,400,401,404,403,406,407,409,408],"class_list":["post-480","post","type-post","status-publish","format-standard","hentry","category-genetics-biology","category-computer-software","tag-cnv","tag-computer-software","tag-genetics-biology","tag-affx","tag-arrays","tag-chip_data","tag-copy-number-variation","tag-gaussian_mixture","tag-genome_science","tag-k_means","tag-nature_paper","tag-normalize","tag-partitioning","tag-ratios","tag-whitepaper"],"_links":{"self":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/480","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/comments?post=480"}],"version-history":[{"count":0,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/480\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/media?parent=480"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/categories?post=480"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/tags?post=480"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}