HI Gaurav

Have you solved your problem?. I am also facing the same problem. I did it
as James mention,but still i m not able to get phenotypic information. Here
is the steps:-

gse <- getGEO(filename='GPL10265/GSE21111_family.soft.gz',GSEMatrix=TRUE)
pData(gse[[1]])  OR phenoData(gse[[1]])
Error in pData(gse[[1]]) :
  error in evaluating the argument 'object' in selecting a method for
function 'pData': Error in gse[[1]] : this S4 class is not subsettable

Thanx


On Thu, May 19, 2011 at 1:32 PM, James F. Reid <
james.reid@ifom-ieo-campus.it> wrote:

> 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
>>
>>
>>
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