[BioC] Trouble with getGEO retrieving dataset

smohapat at vbi.vt.edu smohapat at vbi.vt.edu
Sat May 26 14:56:51 CEST 2007


Thanks for the response. I would use the new version of GEOquery when it
becomes available.



On Fri, May 25, 2007 10:52 pm, Sean Davis wrote:
> Saroj Mohapatra wrote:
>> Hi friends,
>> I am having trouble parsing (it is not a download problem) some GEO
>> datasets using GEOquery. First I was using R 2.4.1 (GEOquery 1.8.0), but
>> the error could be reproduced using R 2.5.0 (GEOquery 2.0.3).
>> In the example below, I could parse dataset GDS1080, but not GDS1082.
>> Is there anything I am doing wrong?
> Hi, Saroj.  You are not doing anything wrong.  GDS1082 is unusual in
> that it contains no SUBSET tags.  I was unaware that such GDS files
> existed, so the code didn't deal with this situation.  I have corrected
> the problem in the development version of GEOquery which should be
> available in the next day or so.  I will be changing the release version
> as well; look for a new version early next week.  Thanks for the bug
> report.
> Sean

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