{"id":444,"date":"2018-07-24T10:59:30","date_gmt":"2018-07-24T17:59:30","guid":{"rendered":"http:\/\/blogs.reed.edu\/compbio\/?p=444"},"modified":"2019-06-14T15:49:28","modified_gmt":"2019-06-14T22:49:28","slug":"week-9-fixing-nodescoring-py","status":"publish","type":"post","link":"https:\/\/blogs.reed.edu\/compbio\/2018\/07\/24\/week-9-fixing-nodescoring-py\/","title":{"rendered":"Week 9: Fixing Nodescoring.py"},"content":{"rendered":"<p>In my last blog post, I talked about how I was concerned about how small the range of normalized node scores is. This week I&#8217;ve been trying to figure out why that is. To do this I&#8217;ve been making histograms of each step of the process from foldchange to Xv to Cv. This is an example of that process for one gene:<\/p>\n<figure id=\"attachment_445\" aria-describedby=\"caption-attachment-445\" style=\"width: 640px\" class=\"wp-caption alignright\"><img loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-445\" src=\"https:\/\/blogs.reed.edu\/compbio\/files\/2018\/07\/FirstFoldChange_Histo.png\" alt=\"\" width=\"640\" height=\"480\" srcset=\"https:\/\/blogs.reed.edu\/compbio\/files\/2018\/07\/FirstFoldChange_Histo.png 640w, https:\/\/blogs.reed.edu\/compbio\/files\/2018\/07\/FirstFoldChange_Histo-300x225.png 300w\" sizes=\"auto, (max-width: 709px) 85vw, (max-width: 909px) 67vw, (max-width: 984px) 61vw, (max-width: 1362px) 45vw, 600px\" \/><figcaption id=\"caption-attachment-445\" class=\"wp-caption-text\">Distribution of foldchanges across patient samples for a single gene.<\/figcaption><\/figure>\n<figure id=\"attachment_446\" aria-describedby=\"caption-attachment-446\" style=\"width: 640px\" class=\"wp-caption alignright\"><img loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-446\" src=\"https:\/\/blogs.reed.edu\/compbio\/files\/2018\/07\/FirstXv_Histo.png\" alt=\"\" width=\"640\" height=\"480\" srcset=\"https:\/\/blogs.reed.edu\/compbio\/files\/2018\/07\/FirstXv_Histo.png 640w, https:\/\/blogs.reed.edu\/compbio\/files\/2018\/07\/FirstXv_Histo-300x225.png 300w\" sizes=\"auto, (max-width: 709px) 85vw, (max-width: 909px) 67vw, (max-width: 984px) 61vw, (max-width: 1362px) 45vw, 600px\" \/><figcaption id=\"caption-attachment-446\" class=\"wp-caption-text\">Distribution of Xvs across patient samples for a single gene<\/figcaption><\/figure>\n<p>The Cv of the gene above was 0.5000000003. Unfortunately, it looks like a lot\u00a0of genes even with fairly different fold change and Xv distributions end up with very similar Cvs.<\/p>\n<p>Ibrahim realized that this is occurring\u00a0because there is an error in the equations we were using so we will have to rethink the way we normalize the data.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>In my last blog post, I talked about how I was concerned about how small the range of normalized node scores is. This week I&#8217;ve been trying to figure out why that is. To do this I&#8217;ve been making histograms of each step of the process from foldchange to Xv to Cv. This is an &hellip; <a href=\"https:\/\/blogs.reed.edu\/compbio\/2018\/07\/24\/week-9-fixing-nodescoring-py\/\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;Week 9: Fixing Nodescoring.py&#8221;<\/span><\/a><\/p>\n","protected":false},"author":1800,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[9,11,1],"tags":[],"class_list":["post-444","post","type-post","status-publish","format-standard","hentry","category-cancer","category-summer-research-2018","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/posts\/444","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/users\/1800"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/comments?post=444"}],"version-history":[{"count":7,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/posts\/444\/revisions"}],"predecessor-version":[{"id":458,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/posts\/444\/revisions\/458"}],"wp:attachment":[{"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/media?parent=444"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/categories?post=444"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/tags?post=444"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}