[BioC] error with accessing GEOquery data

[Kishor Tappita]

Dear Sean,

This information does help me a lot.

Thank you so much.

Regards,
Kishor

On Tue, Sep 1, 2009 at 3:54 PM, Sean Davis<seandavi at gmail.com> wrote:
>
>
> On Tue, Sep 1, 2009 at 5:48 AM, Kishor Tappita <kishor.tappita at gmail.com>
> wrote:
>>
>> Dear All,
>>
>> I am trying to analyze a Microarray series data using "GEOquery". I
>> get the below
>> error when trying to extract the information.
>>
>> > gse = getGEO("GSE15709");
>> > Meta(gse)
>> Error in function (classes, fdef, mtable)  :
>>  unable to find an inherited method for function "Meta", for signature
>> "list"
>> > GSMList(gse)[[1]]
>> Error in function (classes, fdef, mtable)  :
>>  unable to find an inherited method for function "GSMList", for
>> signature "list"
>>
>> Thanks in advance for your help.
>>
>
> getGEO() defaults to GSEMatrix=TRUE.  Per the documentation, this returns a
> list of ExpressionSet objects.  So, gse[[1]] is an ExpressionSet.  The
> accessors that you are using above are for returns from calls to getGEO()
> with GSEMatrix=FALSE.  Unless there is a specific need to get information
> from the full GSE SOFT file, I would recommend staying with GSEMatrix=TRUE
> and working with the more standard ExpressionSet object(s).
>
> Hope that helps.
>
> Sean
>
>