[BioC] Drosophila GeneChip analysis

[Paul Mack]

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