Hi , I have tried to run GOseq on my differential expressed gene list, but when I try to run the following command: GO.wall <-goseq(DEGgenes, pwf, "bosTau4", "ensGene", method= "Wallenius") I get the following error: Error in pwf$DEgenes : $ operator is invalid for atomic vectors Does anyone has experience in solving this issue? Thanks, Fernando

Hi Fernando, I know we've already cleared this up privately, but it's a common question so I thought I'd reply on the mailing list. As of the current version of goseq, it is no longer necessary to pass the DEgenes vector to both the nullp() function and goseq(). The standard workflow is now: pwf = nullp(DEgenes,"bosTau4","ensGene") GO.wall = goseq(pwf,"bosTau4","ensGene") Cheers, Matt On 24/02/2011, at 3:20 AM, Biase, Fernando wrote: > Hi , > > I have tried to run GOseq on my differential expressed gene list, > but when I try to run the following command: > > GO.wall <-goseq(DEGgenes, pwf, "bosTau4", "ensGene", method= > "Wallenius") > > I get the following error: > > Error in pwf$DEgenes : $ operator is invalid for atomic vectors > > Does anyone has experience in solving this issue? > > Thanks, > Fernando > > _______________________________________________ > 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}