[BioC] GEO annotation
sdavis2 at mail.nih.gov
Mon Jun 23 17:29:00 CEST 2008
On Mon, Jun 23, 2008 at 10:46 AM, Roumyana Yordanova
<roumyana.yordanova at bms.com> wrote:
> Thanks. I need class information that can be used in ANOVA type analysis.
> GSE annotation is not well structured as you mentioned.
> GDS have some curated annotation that can be extracted with GEOquery.
> However, the latest GDS is from last year. Any ideas if GDS will be
I have not heard that GDS will not be continued, but your best bet is
to email NCBI GEO directly for those questions.
> Sean Davis wrote:
>>On Wed, Jun 18, 2008 at 11:13 AM, Roumyana Yordanova
>><roumyana.yordanova at bms.com> wrote:
>>>Is there a package in R that downloads any available annotation (e.g. cancer
>>>type, time points, dose, etc.. for each sample) in the GSE series.
>>If you need the information for a single GSE, you can look at the
>>GEOquery package. If you want this for many (or all) data in GEO,
>>look at the GEOmetadb package. Note that, in general, GEO does not
>>curate the annotation and it is often not in a computable form. If
>>you need more details, you could supply a little bit more detail about
>>what you want to do.
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