Talk:Genome-wide association study/GA1

GA Review
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Reviewer: Estevezj (talk · contribs) 02:48, 9 January 2013 (UTC)

I've started my first read-through and will update this review as I proceed. — James Estevez (talk) 02:48, 9 January 2013 (UTC)

Criteria
 Good Article Status - Review Criteria   		A good article is&mdash;  :
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Discussion
Again, fine work on the article. In the course of the review I've made some minor changes to the article to correct for usage, style, and to add a handful of references. I've tagged several statements that require in-line citations under the Good Article criteria.

Moving forward, as work on the article continues I would like to bring to your attention the article available at PLoS Computational Biology. This article is available under the Wikipedia compatible CC-BY license, meaning that figures and text from it can be incorporated in this article. This resource may prove valuable should editors decide to work towards FA status.

Best regards, — James Estevez (talk) 02:26, 18 January 2013 (UTC)


 * Working my way slowly through it. Have a bit at work right now, so apologies for the small steps approach - I will be able to make it in the 14 days though. Today I figured the "there have been two general trends" citation need. First I wanted to claim that this was not needed since the previous paragraphs cites a 2005, n=146 study for main disease phenotype (ARM), and the following 4 citations give later studies that are larger or directed towards more narrowly defined phenotypes. But I think I found an ok article for it now (the Ioannidis et al 2009, nature review one). However, particularly the size statement is so self-evident that it's kinda hard to find stated clearly in reviews. I hope "Consortia of investigators are also becoming increasingly popular" should cover it ok. The defined phenotypes is easier, and it's summed up by the "Phenome mapping" mapping section. Also updated the 200 wellcome trust with a slight re-write that should fix the 'when' mark.--LasseFolkersen (talk) 21:08, 20 January 2013 (UTC)


 * Same way I reviewed it. Anyhow, that's no problem, just let me know if you get slammed and need a bit more time. From what I understand, things that are self-evident to experts getting tagged with is a fairly common point of frustration for people (Expert retention), but I think that'll suffice. Include it in your next GWAS article and problem solved.☺ (I also moved the WTCCC section around a bit.) — James Estevez (talk) 22:38, 20 January 2013 (UTC)


 * Haha, yeah - I'll try to get a short sentence into the next publication "by the way, GWA studies are larger today than in 2007" :-) at least it's hard to argue against. But seriously - no worries. I do understand the need for good sources for this. Got one more citation needed now. That Bush et al that you suggested - its section 6.3 covers the basic P-value thresholds pretty well. Will look at the last citation needed and prose tomorrow--LasseFolkersen (talk) 19:58, 21 January 2013 (UTC)


 * Ok, I figured out the last citation missing and also re-wrote some of that paragraph to address your prose hold. I also removed those extra reviews as by your note 7 - there's plenty of good reviews in the text already. What about the "external links"? I removed some of them now, leaving only the ones I had heard about as main resources often used. For your point about ref-previously-known-as-42/the MacArthur blog, I'll make a note of looking for articles for it later. I'm not sure that one ever came up in official review afterwards, but I'll change it if I find something. Also I wanted to ask you about note 9 - Do you suggest that I remove the horizontal dashed lines, or that I try to explain them in caption? It can't be much more than "the top dashed lines represents the chosen cutoff for significance at p < 5×10^−8, since that's as much as I could get from the article myself. I have no clue why they put in a line at P=10^-5 (and frankly I think it's quite arbitrary). --LasseFolkersen (talk) 21:04, 21 January 2013 (UTC)


 * External links are beyond the scope of the GAC. That said, the guideline (WP:EL) goes into detail, but I see no problem with it as it currently exists. I've reconsidered my note for the lead figure: I think that further detail would probably be better placed in the Manhattan plot (the same image is used to illustrate both articles) caption or in the |image description. If you choose to add it here I suggest dropping the final sentence of the caption ("This example is...") and then tacking on "the top dashed lines represents the chosen cutoff for significance at p < $5$" or some concise variation. In any event, I've passed the article and everything should update once the bot comes through. Thanks again for your work on this. — James Estevez (talk) 22:10, 22 January 2013 (UTC)