Unlike GOstats, goseq does not seem to allow a gene universe. Wouldn't it make more sense to compare the DE genes to all the genes that express in the samples? --Naomi

Hi Naomi, The gene universe is specified by the named vector (your indicator variable from your last post); all the genes in the universe go into the vector names, and values of 1 or 0 show which genes are in your selected list. Cheers, Jenny At 09:31 PM 3/28/2011, Naomi Altman wrote: >Unlike GOstats, goseq does not seem to allow a gene >universe. Wouldn't it make more sense to compare the DE genes to >all the genes that express in the samples? > >--Naomi > >_______________________________________________ >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