[BioC] R: GEOquery and platforms splitting

[Alberto Goldoni]

I agree with you .....i have used GEOquery for GSE files and it works
fine....

You must pay attention when NCBI GEO changed the location of the GSE
files!
Sometimes it appens but Sean has changed GEOquery very rapidly (very
good work).

Best regards

Dr Alberto Goldoni

Medical Genetics Unit

S. Orsola-Malpighi Hospital

Via Massarenti n.9, Pad 11

40100 Bologna, Italy

alberto.goldoni at eurogene.org

www.eurogene.org

www.lagem.it


-----Messaggio originale-----
Da: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] Per conto di Christos
Hatzis
Inviato: giovedì 18 maggio 2006 19.24
A: bioconductor at stat.math.ethz.ch
Oggetto: Re: [BioC] GEOquery and platforms splitting

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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