[BioC] GEOquery and platforms splitting

[Sean Davis]

On 5/18/06 1:23 PM, "Christos Hatzis" <christos at silicoinsights.com> wrote:

> 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.

Hi, Roberta.  Christos has already done a good job of explaining the
situation--GEO does allow multiple platforms and their associated samples
(GSMs) to be lumped together into a single GSE.  In the GEOquery vignette,
there is an example of converting a GSE to an exprSet.  It shows how to do
it with one platform in the GSE.  Doing so for two platforms is the same
except that you need to extract the GPLs individually.  Also, you need to
extract the GSMs associated with each platform separately.  The GPLList(gse)
function will get you the list of GPLs that you can operate on.  The GSMList
will get you a list of GSMs; to extract only those that are associated with
a  given platform, the example in the vignette shows how to extract the
platform information from each GSM in the GSMList.  You can use this
information to pull out the GSMs associated with each GPL.

I admit that this process is not a simple one-line command like for GDSs,
but GEO series are by their very nature complicated and do not lend
themselves very well to a "standard, one-size-fits-all" approach.

Sean

> -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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