[BioC] How to extract Phenotype data from GSE

[James F. Reid]

Hi Reema,

On 07/11/11 03:34, Reema Singh wrote:
> 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

the reason this approach is not working for you is because you are using 
the SOFT file instead of the GSE_MATRIX. With the file 
'GSE21111_series_matrix.txt.gz' the function getGEO will return a list 
of ExpressionSet(s) which you can query for phenotypic data using pData 
or phenoData.
It would be easier to simply use:
  gse <- getGEO("GSE21111")

Best,
J.

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