[BioC] getGEO without platform?
cei at ebi.ac.uk
Wed Jan 21 12:20:27 CET 2009
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.
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.
> Many thanks,
> > sessionInfo()
> R version 2.8.0 (2008-10-20)
> attached base packages:
>  stats graphics grDevices datasets tools utils methods
>  base
> other attached packages:
>  GEOquery_2.6.0 RCurl_0.93-0 Biobase_2.2.1
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