[BioC] extracting phenotypic data from GEO (i.e. GSE8671)

[Martin Morgan]

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

Hi Andrew -- you can save a few keystrokes with

  pData(gse[[1]])

Martin

> 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 at gmail.com> wrote:
> 
>> On Thu, Jun 4, 2009 at 5:41 PM, Andrew Yee<yee at 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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