Dear all,

I currently facing some difficulties in my analysis of a meta-study, and I
figure that I could probably get some valuable suggestions or comments from
you guys. I apologize for this little off topic post.

I am trying to compare the microarray experiments from various groups
(studies), I simply want to get the differentially expressed genes from each
study (they are all from affymetrix), so i used SAM to do the analysis on
each study. To get the differentially expressed genes, I was thinking to use
the same FDR to identify the differentially expressed genes on each study.
However, I figure that there are big differences (eg.  if I pick FDR = 0.05,
there are 1000 differentially expressed genes in one study, and the other
one study would have less than 50 genes). So I would like to ask what other
criteria I should also try to do this kind of meta-analysis, as I want to
compare the results from each of the study.

Thanks a lot. I greatly appreciate for any comment or suggestion

-- 
Lam C. Tsoi (Alex)
Medical University of South Carolina

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