Hi,

I've been using some of the SimpleAffy functions to analyze some GEO
experiments.  I have the following exprSet:

> Data
Expression Set (exprSet) with
        22690 genes
        8 samples
        phenoData object with 1 variables and 8 cases
        varLabels
                tissue: read from file


> pData(Data)
             tissue
GSM73331    control
GSM73332    control
GSM73333    control
GSM73334    control
GSM73335 dystrophic
GSM73336 dystrophic
GSM73337 dystrophic
GSM73338 dystrophic


> res<-pairwise.comparison(Data,"tissue",c("control","dystrophic"),logged=F)
Error in validObject(.Object) : invalid class "PairComp" object: invalid
object for slot "pData" in class "PairComp": got class "factor", should be
or extend class "data.frame"

The problem seems to be in the get.fold.change.and.t.test() function, where
the pData object comes out as a factor for some reason, and thus the new
PairComp object can't be constructed.

I don't have this problem when I read in cel files and phenodata using
ReadAffy, and then use rma() to construct an exprSet.

For the GEO data, I'm constructing the exprSet using the following:

p<-read.table(file=GSE3252_series_matrix.txt,header=T,row.names=1,
comment.char="!")
pheno<-read.phenoData("pdata.txt",sep="\t",header=T,row.names=1)
Data<-new('exprSet',exprs=as.matrix(p),phenoData=pheno)

I would appreciate any insight or help.


Thanks,
Peter Lambert

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