tag:blogger.com,1999:blog-6232819486261696035.post4399939080505009894..comments2023-09-25T09:01:44.323-05:00Comments on Getting Genetics Done: More on the McClellan / King GWAS essayStephen Turnerhttp://www.blogger.com/profile/06656711316726116187noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-6232819486261696035.post-84513911701039275182011-03-29T17:15:04.638-05:002011-03-29T17:15:04.638-05:00It seems like it is much more dense in Europe than...It seems like it is much more dense in Europe than in Africa unless the chart shown above is not to scale.DLOhttp://www.delcowireus.com/dlo_cable.phpnoreply@blogger.comtag:blogger.com,1999:blog-6232819486261696035.post-87686862641441534132011-02-16T16:02:34.669-06:002011-02-16T16:02:34.669-06:00How do I may plot this figura using R (alleles fre...How do I may plot this figura using R (alleles frequency over the world map)?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6232819486261696035.post-51185087493980772312010-05-20T19:42:48.854-05:002010-05-20T19:42:48.854-05:00What does a community of fairly narrowly trained f...What does a community of fairly narrowly trained folks do...if the one approach they know well falls out of fashion. The U.S. solution is "off with their heads."<br /><br /><br />Or, start sequencing. The last bastion of the sinner.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6232819486261696035.post-1506236337487688462010-05-03T13:00:23.468-05:002010-05-03T13:00:23.468-05:00I agree there are interesting problems with the pa...I agree there are interesting problems with the paper...however there is also a "too big to fail/bubble" aspect to GWAS and many other systems biology approaches. At a recent conference in Oxford one of the science/phil folks raised the point: "one thing that systems approaches definitely do is concentrate resources at large centres"...so..not to pick on the picked on...what does a community of fairly narrowly trained folks do...if the one approach they know well falls out of fashion. A lot of 80s era organismal/biochemist types might have some wisdom to share...short answer..the U.S. solution is "off with their heads"..not fun.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6232819486261696035.post-36722027733321338292010-04-29T13:28:20.180-05:002010-04-29T13:28:20.180-05:00I have really enjoyed reading all of the commentar...I have really enjoyed reading all of the commentary about this article provided on this blog and other linked blogs. Overall - I feel the authors fail to recognize the process that is science ... sure we might not know the functionality right now - but many of the replicated GWAS signals are clearly very robust associations and deserve to be explored further. For example, it wasn't that long ago that the ENCODE project provided evidence of the pervasively transcribed genome, nearly eliminating the term "junk DNA" from having any meaning. Who knows what we might learn in a few years after pursuing the GWAS hits? <br /><br />While a thought provoking article, I think it is filled with justification and support for their own underlying research agenda.Kristin Meyersnoreply@blogger.comtag:blogger.com,1999:blog-6232819486261696035.post-9356782908459760722010-04-29T10:26:20.771-05:002010-04-29T10:26:20.771-05:00Thanks for opening a new thread for discussion. I ...Thanks for opening a new thread for discussion. I realized that Toscani population is actually part of HapMap3, so the allele frequency can be inferred from there (n=102, still small but good enough). I assumed that "Toscani in Italia" in HapMap is similar to "Tuscan Italy" in HGDP. The MAF (C allele) is indeed 41% in HapMap sample (202 chromosomes, hapmap 3 release 3, ftp://ftp.sanger.ac.uk/pub/hapmap3/r3/hapmap3_r3_b36_fwd.qc.poly.tar.gz), which is fairly similar to European Americans and not even remotely close to the 77% number inferred from n=7 by McClellan et al.<br /><br />This exercise represents a particularly dramatic example how small sample size in whole-genome data can lead to biased estimates and conclusions. It also teaches us that rigorous scientists should always quantify the uncertainty of results, or at least present a sample size/power. Failing to do that, we would be merely fooling ourselves and the readers outside of the community.Kai Wangnoreply@blogger.com