Dear Sean

Thanks for the reply

I tried the way you have suggested but again it gave me an error

gse6901.eset <- getGEO("GSE6901")[[1]]


Error in validObject(.Object) :
  invalid class "ExpressionSet" object: featureNames differ between
assayData and featureData

Check the version of R and other packges which are updated to newer version

Wishes

Hemant

On Tue, Sep 9, 2008 at 12:52 AM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> On Mon, Sep 8, 2008 at 2:37 PM, hemant ritturaj
> <ritturajhemant@gmail.com> wrote:
> > Dear all,
> >
> > I was trying to make expression set from the GSE data
>
> This will get you an ExpressionSet:
>
> gse6901.eset <- getGEO("GSE6901")[[1]]
>
> Now, gse6901.eset is an ExpressionSet.  No need for all the code
> below.  The [[1]] is needed because getGEO() on a GSEMatrix returns a
> list of ExpressionSets.  In this particular case, there is only one
> ExpressionSet, so we choose it.
>
> Sean
>
> > Following is the code
> >
> > gse6901 <- getGEO("GSE6901", GSEMatrix=F)
> > probesets <- Table(GPLList(gse6901)[[1]])$ID
> > data.matrix <- log2(do.call("cbind", lapply(GSMList(gse6901), function(x)
> {
> > + tab <- Table(x)
> > + mymatch <- match(probesets, tab$ID_REF)
> > + return(as.numeric(tab$VALUE[mymatch]))
> > + })))
> > rownames(data.matrix) <- probesets
> > colnames(data.matrix) <- names(GSMList(gse6901))
> > pdata <- data.frame(samples = names(GSMList(gse6901)))
> > rownames(pdata) <- names(GSMList(gse6901))
> > pheno <- new("phenoData", pData = pdata, varLabels = as.list("samples"))
> >
> >
> > Error: The phenoData class is defunct, use AnnotatedDataFrame (with
> > ExpressionSet) instead
> >
> > I am not able to understand what function has exactly gor changed in
> Biobase
> > module as I tried
> >
> > pheno <- new("AnnotatedDataFrame", pData = pdata, varLabels =
> > as.list("samples"))
> >
> > then again got an error
> >
> > Error in .nextMethod(.Object, ...) :
> >  invalid names for slots of class "AnnotatedDataFrame": pData, varLabels
> >
> > Kindly anyone please help me sorting out this error, I shall be very
> > thankful for your kind help
> >
> > Regards
> > --
> > Hemant Ritturaj Kushwaha
> >
> >        [[alternative HTML version deleted]]
> >
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> >
>

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