[BioC] subsetting exprsSet

Beth Wilmot wilmotb at ohsu.edu
Sat Dec 4 00:51:17 CET 2004

Windows 2000
I have a normalized Expression Set with 2 variables (sample and
 Expression Set (exprSet) with 
        54675 genes
        17 samples
                 phenoData object with 2 variables and 17 cases
                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.  

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