{"id":23885,"date":"2010-08-23T23:05:30","date_gmt":"2010-08-24T07:05:30","guid":{"rendered":"http:\/\/blogs.discovermagazine.com\/gnxp\/?p=5855"},"modified":"2010-08-23T23:05:30","modified_gmt":"2010-08-24T07:05:30","slug":"just-pushing-buttons","status":"publish","type":"post","link":"https:\/\/www.razib.com\/wordpress\/2010\/08\/23\/just-pushing-buttons\/","title":{"rendered":"Just pushing buttons"},"content":{"rendered":"<p><a href=\"http:\/\/scienceblogs.com\/mikethemadbiologist\/\">Mike the Mad Biologist<\/a>, whose bailiwick is the <a href=\"http:\/\/scienceblogs.com\/mikethemadbiologist\/microbiome\/\">domain of the small<\/a>, asks in the <a href=\"http:\/\/blogs.discovermagazine.com\/gnxp\/2010\/08\/genetic-variation-within-africa-and-the-world\/#comment-32269\">comments<\/a>:<\/p>\n<blockquote>\n<p>I don&#8217;t mean to bring up a tangential point to the post, but why does the field of human genetics use PCA to visualize relationships?  When I see plots like those shown here that have a &#8216;geometric pattern&#8217; to them (the sharp right angles;  another common pattern is a Y-shape), that tells me that there are lots of samples with zeros for many of the Y-variables (i.e., alleles that are unique to certain populations).  Thus, the spatial arrangement of the points is largely an artifact of an inappropriate method:  how does one calculate a correlation matrix when many of things one is correlating have values of zero?<\/p>\n<p>If one really was keen on using PCA, one could calculate a pairwise distance matrix and then use that instead of the correlation matrix (Principal Coordinates Analysis).<\/p>\n<\/blockquote>\n<p>Since I know some human geneticists do read this weblog, I thought it was worth throwing the question out there.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Mike the Mad Biologist, whose bailiwick is the domain of the small, asks in the comments:<br \/>\nI don&#8217;t mean to bring up a tangential point to the post, but why does the field of human genetics use PCA to visualize relationships?  When I see plots like those shown here that have a &#8216;geometric pattern&#8217; to [&#8230;]<\/p>\n","protected":false},"author":12,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[584,4,585,586],"tags":[],"class_list":["post-23885","post","type-post","status-publish","format-standard","hentry","category-analysis","category-genetics","category-pca","category-tools"],"_links":{"self":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/23885","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/users\/12"}],"replies":[{"embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/comments?post=23885"}],"version-history":[{"count":4,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/23885\/revisions"}],"predecessor-version":[{"id":24114,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/23885\/revisions\/24114"}],"wp:attachment":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/media?parent=23885"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/categories?post=23885"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/tags?post=23885"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}