On Fri, Oct 5, 2012 at 1:40 PM, Sylvain Foisy
<Sylvain.Foisy@inflammgen.org>wrote:

> Hi,
>
> I am so not a R expert so I apologize for the newbie question... If I have
> a list of gene symbols, can I get, for each of them, all GEO profiles for
> that gene across all platforms (or a subset of), extract normalized gene
> expression for that gene and feed this to LIMMA or the like to observe
> differential expression and make a list of all Datasets where this gene is
> differentially expressed?
>
>
Hi, Sylvain.

Sorry for the late reply.  You can use GEOquery to download entire datasets
as you see fit.  As for differential expression, that is trickier since you
will need to define a way to examine the metadata for each GEO dataset to
determine what to use for defining groups for testing for differential
expression.  A secondary concern is that the GEO platform files do not
contain standard columns, so there is no guarantee that a gene identifier
exists or how you would find such a column programmatically if it did.

Sean


> Sorry if this seems stupid; I promised to document any solution in our
> wiki and share it with the world ;-)
>
> Best regards
>
> Sylvain
>
> ==============================================================
> Sylvain Foisy, Ph. D.
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