Hi, I'm also interested in this question. How would you recommend handling replicates? For example, if you had counts for each of three control samples and each of three treatments, would it make sense to run "sage.test" for every combination, get a p value for each test, and then combine them somehow? -Ann On Wed, Mar 7, 2012 at 9:30 AM, Naomi Altman <naomi at="" stat.psu.edu=""> wrote: > Look at package sagenhaft, function sage.test. > > --Naomi > > At 04:40 AM 3/7/2012, Alyaa Mahmoud wrote: >> >> Dear Group >> >> I would like to perform a pairwise comparisons using fisher exact test for >> 5 samples (columns) and 3835 genes (rows). Is there a way I can do the >> pairwise comparison at one time ? >> >> I would highly appreciate any help >> Thanks a lot >> >> yours, >> Alyaa Mahmoud >> >> -- >> Alyaa Mahmoud >> >> "Love all, trust a few, do wrong to none"- Shakespeare >> >> ? ? ? ?[[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor