[BioC] analyse GSM files form GEO repository

Sean Davis sdavis2 at mail.nih.gov
Tue Jun 14 18:43:04 CEST 2011

On Tue, Jun 14, 2011 at 10:34 AM, nac <nac at sanger.ac.uk> wrote:
> Hi,
> I would like to re-analyse some array files which are in the GEO
> repository. These are illumina bead array expression data. Once I have
> downloaded the GSM file, is there a pacakge I can use that can handle these
> data? I look for basic information on the detection levels ( like the
> BeadStudio software)? I saw the beadarray pacakge which has a lot of
> function, has somebody some experience with this package and could give me
> some advise on how to get these basic data?
> many thanks

Hi, Natalie.  You'll need to look at the files available from GEO.
There may be a supplemental file that is in a format that beadarray
understands.  Alternatively, you could get the data using the GEOquery
package and extract the information you need from the GEO files.
Unfortunately, it will be up to you to figure out what information GEO
provides.  If you need a bit more help, you could try sending the GEO
accessions to the list and perhaps someone can help you determine what
file formats are available and how they might best be handled.


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