[BioC] Drosophila GeneChip analysis

[Arne.Muller at aventis.com]

do you have a factorial design, and you run one linear model for each gene, and then looking at the p-values for the coefficients? Could you give some more information about what you're doing, I'm not sure I understand ...?

	regards,

	Arne

--
Arne Muller, Ph.D.
Toxicogenomics, Aventis Pharma
arne dot muller domain=aventis com

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Paul Mack
> Sent: 14 May 2004 16:20
> Subject: [BioC] Drosophila GeneChip analysis
> 
> 
> 
> I am in the midst of analyzing Affymetrix Drosophila GeneChip 
> data using 
> RMA such that separate regression lines are estimated for 
> each gene. It was 
> recommended to me that I use a p-value of .0001 as a cutoff 
> for the effect 
> estimates rather than try to apply Bonferroni or other multiple test 
> corrections. Lately, however, I have begun to wonder if 
> others doing this 
> sort of analysis use similar cutoffs and, in general, what 
> others think 
> about statistical stringency in this situation. Any help will be most 
> appreciated; I will summarize any replies that I get that are 
> not sent 
> directly to the list. Thank you.
> 
> 
> Paul Mack, Ph.D
> Department of Genetics
> University of Georgia
> Athens, GA
> USA
> 
> 706-542-1578 (w)
> 706-542-3910 (fax)
> paulmack at arches.uga.edu
> 
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