Dear R-Users, Thanks to your help I found some helpful informations. However, I still have some doubts about how to use GO. What I should do first? I should do non-specific filtering or gene selection via t-test? Is it better to do gene filtering on normalized on non-normalized data? Regards, Barbara Cegielska

Do a t-test or similar using limma to find your differentially expressed gene list. Then put this gene list into something like GOStats or topGO in bioconduictor, or David, Fatigo or Fatiscan online ________________________________ From: bioconductor-bounces@stat.math.ethz.ch on behalf of Barbara Cegielska Sent: Fri 03/07/2009 8:58 AM To: bioconductor at stat.math.ethz.ch; r-help-bounces at r-project.org Subject: [BioC] neverending GO problems Dear R-Users, Thanks to your help I found some helpful informations. However, I still have some doubts about how to use GO. What I should do first? I should do non-specific filtering or gene selection via t-test? Is it better to do gene filtering on normalized on non-normalized data? Regards, Barbara Cegielska _______________________________________________ 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