Hi James, probeSetSummary2(hgOver) works well as long as there are no NA's in this particuar step: list1<- (unlist(mget(selectedgenes,ath1121501ACCNUM,))) In the presence of NA's, then probeSetSummary2(hgOver) gives me this warning Warning message: The vector of geneIds used to create the GOHyperGParamsobject was not a named vector. If you want to know the probesets that contributed to this result either use a named vector for gene Ids, or pass a vector of probeset IDs via sigProbesets. And then most GO terms go missing in the result. What do I do in such a case?

Hi Sandy, You cannot do a GO test for unannotated reporters. In other words, if you have a probeset that measures some unknown thing, then you cannot use that probeset because there won't be any GO terms associated with it. What happens if you do list1 <- list1[!is.na(list1)] first? Best, Jim On Friday, October 25, 2013 8:47:21 AM, Sandy wrote: > > > Hi James, > > probeSetSummary2(hgOver) works well as long as there are no NA's in this > particuar step: > > list1<- (unlist(mget(selectedgenes,ath1121501ACCNUM,))) > > In the presence of NA's, then probeSetSummary2(hgOver) gives me this warning > > Warning message: > The vector of geneIds used to create the GOHyperGParamsobject was not a > named vector. > If you want to know the probesets that contributed to this result > either use a named vector for gene Ids, or pass a vector of probeset IDs > via sigProbesets. > > > And then most GO terms go missing in the result. > > What do I do in such a case? > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099