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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]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor 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