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Hi Chanchal, Unless you can give us a small reproducible example that shows what you are talking about, there is really nothing anybody can do about this. Best, Jim Chanchal Kumar wrote: > Dear All, > > > > I have been using the "GOstats" package for the GO enrichment on my > dataset. I have two cluster of genes(test1, test2) and a reference > set(universe set). After doing enrichment on the two sets for GO BP > w.r.t to the universe set I get a list of enriched terms. In both cases > I get "Cell Cycle" (GO:0007049) as enriched. Till there it's fine. But > strangely I see that the Category Size ( "Size" column of the output ) > gives me different numbers for Cell cycle annotated genes in my universe > set( in test1 77, in test2 366). Now my concern is that given I use the > same universe set how I can get different numbers of Cell cycle > annotated universe genes? This is just one example and I see these > inconsistencies for many common terms. > > > > Any insights on this problem will be very helpful. > > > > Best Regards, > > Chanchal > > =============================== > > Chanchal Kumar, Ph.D. Candidate > > Dept. of Proteomics and Signal Transduction > Max Planck Institute of Biochemistry > Am Klopferspitz 18 > 82152 D-Martinsried (near Munich) > Germany > e-mail: chanchal at biochem.mpg.de > Phone: (Office) +49 (0) 89 8578 2296 > > Fax:(Office) +49 (0) 89 8578 2219 > http://www.biochem.mpg.de/mann/ > =============================== > > > > > [[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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623