[BioC] getGEO without platform?

[Cei Abreu-Goodger]

Hi Sean,

Thanks for your answer, I wasn't aware of that problem. Do you mean then 
that you may get different featureNames for different experiments from 
the same platform? That would definitely be a problem. Do you know if 
there's a way to restrict the annotation download to fewer fields, or 
download it in a compressed form?

For a few random "GSE" that I checked, the "*_series_matrix.txt.gz" 
files do contain the correct probeset names in the "ID_REF" column. If 
this is the case at least for the common Affy platforms, then the option 
of not downloading the AnnotGPL (with a warning?) would still be very 
useful for me.

Thanks again,

Cei


Sean Davis wrote:
> 
> 
> On Tue, Jan 20, 2009 at 6:26 AM, Cei Abreu-Goodger <cei at ebi.ac.uk 
> <mailto:cei at ebi.ac.uk>> wrote:
> 
>     Hi all,
> 
>     I was wondering if there's a way to use getGEO to end up with an
>     ExpressionSet without platform annotation. Why? I have lots of GEO
>     entries from which I want to quickly extract the exprs values, and I
>     don't care about the annotation (and I can always download it later on).
> 
>     I've been trying:
> 
>     geo <- getGEO("GSE11899", GSEMatrix=TRUE, AnnotGPL=FALSE)
> 
>     But for "GSE" ids it seems to ignore the AnnotGPL flag and goes
>     ahead to download 38.1 Mb (in this case) of text annotation!
> 
> 
> Not currently, no.  I can add it for the next release.  However, note 
> that there is no standard for the featureNames in GEO, so you will not 
> always get useful probe names without the annotation.
> 
> Sean
> 
>  
> 
> 
> 
>     Many thanks,
> 
>     Cei
> 
>      > sessionInfo()
>     R version 2.8.0 (2008-10-20)
>     i386-apple-darwin8.11.1
> 
>     locale:
>     en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
> 
>     attached base packages:
>     [1] stats     graphics  grDevices datasets  tools     utils     methods
>     [8] base
> 
>     other attached packages:
>     [1] GEOquery_2.6.0 RCurl_0.93-0   Biobase_2.2.1
> 
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>