[BioC] sample size estimation in genome wide association studies /packages

alex lam (RI) alex.lam at bbsrc.ac.uk
Tue Jan 29 18:09:47 CET 2008

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 C. Lam
Roslin Institute (Edinburgh)
EH25 9PS
United Kingdom
Tel: +44 131 5274471

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-----Original Message-----
From: bioconductor-bounces at 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
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

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 ??



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