After some e-mail exchanges with Sean, this is what finally works:
gse <- getGEO('GSE8671',GSEMatrix=TRUE)
pheno.df <- pData(phenoData(gse[[1]]))

Note that in this example, gse is not a GSE object anymore.  It is a list
of ExpressionSets (in this case one expression set).

(Also note that I'm running R 2.9.0 on a Windows machine using GEOquery
version 2.8.0).

Thanks,
Andrew

On Thu, Jun 4, 2009 at 5:46 PM, Sean Davis <seandavi@gmail.com> wrote:

> On Thu, Jun 4, 2009 at 5:41 PM, Andrew Yee<yee@post.harvard.edu> wrote:
> > Hi, I've been working with the GEOquery package.  I'm interested in
> creating
> > a phenotypic data file from GSE8671.  I imagine this should be possible
> > after using getGEO(), however, it appears to be taking a substantial
> amount
> > of time to parse through the soft file.  Is there a simpler, quicker
> method
> > of extracting just the phenotypic information?
>
> Hi, Andrew.  You didn't post your sessionInfo(), but in recent
> versions of GEOquery, the default is to parse the GSEMatrix files when
> getting GSEs.  This is quite a bit faster (typically taking a few
> seconds for parsing).
>
> Sean
>

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