[BioC] GEOquery and platforms splitting

[Christos Hatzis]

This is not a "problem" per se but several datasets can have data from
multiple platforms.  In fact, Sean Davis wrote in the vignette for GEOquery
that "the GSE is the most confusing of the GEO entries ... [it] can
represent an arbitrary number of samples run on a arbitrary number of
platforms."

One potential solution is to use the GEOquery package.  It will
automatically download GSE files and produce a list of GSM objects and a
list of GPL objects.  These can then be used to produce a datatable for a
single exprset or to construct different datatables for each platform. 

I haven't tested this functionality extensively.  From my limited testing,
GEOquery works great with GDS files, which are hand-curated files.  However
I had mixed success with GSE files.

So I would suggest that GEOquery is your best bet.

-Christos

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Peter (BioC)
Sent: Thursday, May 18, 2006 10:42 AM
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] GEOquery and platforms splitting

Bosotti, Roberta [Nervianoms] wrote:
> Hi all,
> 
> I downloaded a GSE file from GEO using GEOquery. The GSM file contain 
> two "platforms": GPL96 and GPL97. I need to make two separate exprset 
> from the two (the GSMs are not contiguous for the two platforms, but 
> are mixed). Do you have any suggestion on how I could make it?
> 
> Thanks in advance, Roberta

Interesting - what was the GSE number?  That would be very helpful to try
and reproduce the problem.

Peter

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