On Wed, Jan 21, 2009 at 6:20 AM, Cei Abreu-Goodger <cei@ebi.ac.uk> wrote:

> 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.
>

If you restrict yourself to Affy, you are probably OK.

The AnnotGPL argument is used to choose which GPL is used when getting GDS
information.  The NCI GEO staff produces so-called Annotation GPL files for
the GDS subset of GEO.  These annotation GPL files contain different content
from the normal GPL.  However that content is standardized.  The AnnotGPL
simply chooses which will be used.

Sean



>
> Sean Davis wrote:
>
>>
>>
>> On Tue, Jan 20, 2009 at 6:26 AM, Cei Abreu-Goodger <cei@ebi.ac.uk<mailto:
>> cei@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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>>
>>
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