[BioC] Trouble with getGEO retrieving dataset

Sean Davis sdavis2 at mail.nih.gov
Sat May 26 04:52:00 CEST 2007

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.


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