[R] Reading raw intensity data from getGEO's gse object

Martin Morgan mtmorgan at fhcrc.org
Thu Feb 11 20:25:52 CET 2010

On 02/11/2010 10:35 AM, Dipen wrote:
> Hello, I am trying to download a SOFT matrix file for GSE series to extract
> raw intensity data.
> gse<- getGEO('GSExxxx', AnnotGPL=T)
> However, I am not able to use the function Table(gse), which returns the
> following error
>>>> Error in function (classes, fdef, mtable)  : 
>   unable to find an inherited method for function "Table", for signature
> "GSE"
> If I try to use the GDSxxxx file, I get only the adjusted log 2 ratio of
> intensities.
> Is there any way to get to the raw intensity data contained within GSE
> object?

Hi Dipen -- please ask questions about Bioconductor packages on the
Bioconductor mailing list.


Include the output of sessionInfo(), but try updating packages as
outlined at


before posting; I believe this is a known issue that has been addressed.


> Thanks,
> Dipen

Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

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