[BioC] GEOquery and Sample Subsets

[Thomas H. Hampton]

Exactly!

Thanks.

________________________________________
From: seandavi at gmail.com [seandavi at gmail.com] on behalf of Sean Davis [sdavis2 at mail.nih.gov]
Sent: Tuesday, June 04, 2013 12:54 PM
To: Thomas H. Hampton
Cc: bioconductor at r-project.org
Subject: Re: [BioC] GEOquery and Sample Subsets

On Tue, Jun 4, 2013 at 12:38 PM, Thomas H. Hampton
<Thomas.H.Hampton at dartmouth.edu> wrote:
> I am using to GEOquery to establish sample subsets of GEO data -- that is, I would
> like to know which samples are replicates.
>
> I am doing it something like this:
>
> gds505 <- getGEO("GDS505")
> Columns(gds505)
>
>> str(Columns(gds505))
> 'data.frame': 17 obs. of  4 variables:
>  $ sample       : Factor w/ 17 levels "GSM11805","GSM11814",..: 2 4 5 7 9 10 12 14 16 1 ...
>  $ disease.state: Factor w/ 2 levels "normal","RCC": 2 2 2 2 2 2 2 2 2 1 ...
>  $ individual   : Factor w/ 10 levels "001","005","011",..: 6 4 1 2 3 5 8 9 10 6 ...
>  $ description  : chr  "Value for GSM11814: C035 Renal Clear Cell Carcinoma U133A; src: Trizol...
>
> The problem I have is that the getGEO command retrieves a rather large object:
>
>> print(object.size(gds505), units="Mb")
> 12.6 Mb'
>
> This takes up a lot of time and bandwidth if you plan to do it for thousands of accessions.
>
> Is there a way to retrieve less?

Hi, Tom.  Are you saying that you really want just the metadata to
start; in other words, you just want the sample information without
the expression values?

Sean


> I am happy to use R, BioConductor, bioperl or whatever.
>
> Best,
>
> Tom
>
>
>
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>
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