R1.9.1 Windows 2000 Hello, I have a normalized Expression Set with 2 variables (sample and status). Expression Set (exprSet) with 54675 genes 17 samples phenoData object with 2 variables and 17 cases varLabels sample: arbitrary numbering Subsetting for status: 1) test<-eset[,eset$status=="C"] gives me Error in validObject(.Object) : Invalid "phenoData" object: FALSE 2) ext<-c('a','b',c','d') test<-eset[,ext] where ext is a list of my exprSet columns (rows in pData) gives me the error: Error in validObject(.Object) : Invalid "phenoData" object: FALSE The mailing list archives suggest 2). And I have tested it on the eset that is in Biobase and both the method 1) and 2) work fine with the Biobase eset, but not with my exprsSet. Thanks, Beth [[alternative HTML version deleted]]