[BioC] problem with GDS2eSet in GEOquery package

Sean Davis sdavis2 at mail.nih.gov
Sun Jun 10 14:31:41 CEST 2007

Sergii Ivakhno wrote:
> Dear Biocondcutor users 
> Can someone help me with the following problem?
> I use GEO query to fetch a GDS record from GEO and then I use GDS2eSet to export it into exppressionset. According to the source code GDS2eSet also retrieves GPL record   
>     if(is.null(GPL)) {
>       GPL <- getGEO(Meta(GDS)$platform)
>     }
> When the GPL is downloaded I get the following error:
> File stored at:
> /tmp/RtmpMbEluC/GPL570.soft
> Error in validObject(.Object) : invalid class "AnnotatedDataFrame" object:
>   AnnotatedDataFrame colnames of data differ from row.names of varMetadata
> Execution halted
> Interestingly, but I do not get this error on Windows (only linux)
> Thanks a lot in advance.
Hi, Sergii.  Could you let me know what version you are using by giving 


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