sample size estimation in genome wide association studies / packages
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@phguardiolaolcom-152
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@richard-pearson-1304
Last seen 7.8 years ago
Hi Philippe I'm certainly no expert on this, but you might want to look at the Wellcome Trust Case Control Consortium paper from last year: http://www.nature.com/nature/journal/v447/n7145/abs/nature05911.html They have a discussion of sample size (see, e.g. Figure 6), and I believe concluded that without the thousands of samples they used, they wouldn't have detected many of the associations they did find. So yes, 50 could really be way too few. Best regards Richard. phguardiol at aol.com wrote: > Dear Bioconductor users, > > I would like to get "the feeling" of experts dealing with SNP microarrays regarding sample size estimation in genome wide association studies. > Some of the physicians / doctors who would like to perform such studies are asking me about sample size estimation, that is to say?the minimal?number of?chips to be run so that the analysis will?bring... let say positive results. > > My point of view is that in these studies we are more likely to generate hypothesis than to test hypothesis, so that the question of sample size?does not seem to be appropriate for me. > However,?running 50 chips for this kind of study could be really too short. > > I have read again all the papers published in the new england journal of medicine in 2007 and I have not found anything about this question of sample size... or minimal number of chips. > > Point of view of experts would be greatly appreciate. > > If this issue is "real" which package would you recommend for this kind of estimation ?? > > Thanks > > > Philippe?G > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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alex lam RI ▴ 310
@alex-lam-ri-1491
Last seen 7.8 years ago
Hi Phillipe, You mean how many samples you need in a case-control GWA? If yes, read this article: Genome-wide association studies: theoretical and practical concerns. Wang WY, Barratt BJ, Clayton DG, Todd JA. Nat Rev Genet. 2005 Feb;6(2):109-18. Alex -------------------------------------------- Alex C. Lam Roslin Institute (Edinburgh) Midlothian EH25 9PS United Kingdom Tel: +44 131 5274471 Roslin Institute is a company limited by guarantee, registered in Scotland (registered number SC157100) and a Scottish Charity (registered number SC023592). Our registered office is at Roslin, Midlothian, EH25 9PS. VAT registration number 847380013. The information contained in this e-mail (including any attachments) is confidential and is intended for the use of the addressee only. The opinions expressed within this e-mail (including any attachments) are the opinions of the sender and do not necessarily constitute those of Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of phguardiol at aol.com Sent: 29 January 2008 16:02 To: Bioconductor at stat.math.ethz.ch Subject: [BioC] sample size estimation in genome wide association studies /packages Dear Bioconductor users, I would like to get "the feeling" of experts dealing with SNP microarrays regarding sample size estimation in genome wide association studies. Some of the physicians / doctors who would like to perform such studies are asking me about sample size estimation, that is to say?the minimal?number of?chips to be run so that the analysis will?bring... let say positive results. My point of view is that in these studies we are more likely to generate hypothesis than to test hypothesis, so that the question of sample size?does not seem to be appropriate for me. However,?running 50 chips for this kind of study could be really too short. I have read again all the papers published in the new england journal of medicine in 2007 and I have not found anything about this question of sample size... or minimal number of chips. Point of view of experts would be greatly appreciate. If this issue is "real" which package would you recommend for this kind of estimation ?? Thanks Philippe?G [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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