[BioC] How to extract Phenotype data from GSE

[James F. Reid]

Hi Gaurav,

just use phenoData(gse3149[[1]]) to get an 'AnnotatedDataFrame' or 
pData(gse3149[[1]]) to get a data.frame.

HTH.
J.

On 05/19/2011 08:36 AM, Gaurav Kumar wrote:
> Dear Sean and bioconductor users,
>
> I’m new to GEOquery and things are not very clear to me as my
> understanding is limited for the package. I need to know phenotypic
> data for GSE3149. After reading GEOquery manual and mail-archive. I
> did following to find the Phenotypic information for GSE3149.
>
>> gse3149<-getGEO(filename='D:/GSE3149/GSE3149_series_matrix.txt.gz', GSEMatrix=TRUE)
>
>> phenotype<- pData(phenoData(gse3149[[1]]))
> Error in function (classes, fdef, mtable)  :
>    unable to find an inherited method for function "phenoData", for
> signature "factor"
> Error in pData(phenoData(gse3149[[1]])) :
>    error in evaluating the argument 'object' in selecting a method for
> function 'pData'
>
> However, I can see phenoData through show function (>  show(gse3149))
>
> Please, guide me where i’m doing wrong.
> Thanks in advance
> Gaurav
>
>