[BioC] The criteria to be used in a meta-study by using SAM

[Naomi Altman]

I think it would be better to use the list of top 10, 20, ... DE 
genes, rather than to rely on FDR.

--Naomi

At 04:45 PM 8/5/2007, Alex Tsoi wrote:
>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
>
>         [[alternative HTML version deleted]]
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111