Hi Jenny, As Heidi says, this really should work with org packages. Please let me know if you find a case where it doesn't. And, in that case, please send me a specific example so that I can fix it. Marc Heidi Dvinge wrote: > <snip> > > >> Mainly my >> question is why does the GOstats hyperGTest() require a chip- specific >> annotation package when you have to input EntrezGene IDs (the >> mapping key for the org.Xx.eg.db packages), not probe set >> IDs? Could hyperGTest() be (easily) modified to directly accept the >> org.Xx.eg.db packages? >> >> > It already does :) At least when I use hyperGTest() from the Category > package for GO/KEGG/Chrlocation, it works fine with org.Mm.eg.db. I > actually don't know whether there are any differences between hyperGTest() > from GOstats and the one from Category. > > Cheers > \Heidi > > >> Thanks, >> Jenny >> >> Jenny Drnevich, Ph.D. >> >> Functional Genomics Bioinformatics Specialist >> W.M. Keck Center for Comparative and Functional Genomics >> Roy J. Carver Biotechnology Center >> University of Illinois, Urbana-Champaign >> >> 330 ERML >> 1201 W. Gregory Dr. >> Urbana, IL 61801 >> USA >> >> ph: 217-244-7355 >> fax: 217-265-5066 >> e-mail: drnevich at illinois.edu >> >> _______________________________________________ >> 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 >> >> > > _______________________________________________ > 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 > >