On Tue, Oct 12, 2010 at 4:51 AM, Georgia Tsiliki <g_tsiliki@hotmail.com>wrote:

>  Dear Dr Davis,
> I am a biostatistician at BRFAA, Athens. I am currently using the
> 'GEOquery' package with Bioconductor/R. I had a problem with GSE3494 series;
> particularly, i cannot download the 'Data Table of the Clinicopathological
> variables of the Upsala cohort header description' and the 'GEO Sample
> accession numbers and associated Patient IDs header description' files. Both
> of them are included in the GEO accession Viewer with an option to download
> them, but I'm not sure how i can do that via the GEOquery package. I don't
> think there's a soft file for that particular series, do you think that
> might be the problem?
>
>
Hi, Georgia.

I realized a few months ago that this GSE (and others like it) existed.  I
added a function to GEOquery to grab the GSE data tables.  In the case of
GSE3494, there are two of these data tables, so the function will return a
list of two data.frames.

gsedt = getGSEDataTables('GSE3494')

Now, gsedt is a list of length 2 and holds each of the GSE data tables in
the list.  You can use getGEOSuppFiles to get the actual raw data.  With the
two pieces, it is not difficult to generate an ExpressionSet using the
normal affy/Bioc tools.

Hope that helps.

Sean



> Thank you very much for your time,
> Georgia Tsiliki
>

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