[BioC] GEOquery & GDS2eSet error

[Sean Davis]

On 2/14/06 10:30 AM, "Morten Mattingsdal"
<morten.mattingsdal at student.uib.no> wrote:

> Hello everyone,
> Im using GEOquery to retriveve several breast cancer datasets from the
> GEO database.
> The conversion to the LIMMA object MA goes fine for two-color data, but
> Im having difficulties with making an exprSet from the affymetrix data
> retrieved. The function GDS2eSet returns:
> 
> "Error in validObject(.Object) : invalid class "exprSet" object:
> sampleNames different from names of phenoData rows"
> 
> I have tried several different datasets and this error seems very common.
> Is this an annotation problem in the GEO database or my fault ?

Not your fault.  This is due to a recent change in the way that exprSets
validate their slots when creating a new exprSet object.  I have fixed the
problem and committed the changes to BioConductor.  They should be available
in the next 24 hours or so in the development repository.

Sean