[BioC] error with accessing biomaRt attributes

[Kishor Tappita]

Dear Steve,

Thank you for your reply. You are right I am trying to convery Affy Id
to entrez gene ID. Passing the filters parameter to the query solved
my problem.

Below is the modified query.

getBM(attributes = "entrezgene",values =
c("1007_s_at","1053_at","1552256_a_at"),filters=
"affy_hg_u133_plus_2",mart =ensembl)


Thanks,
Kishor

On Wed, Sep 16, 2009 at 8:15 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> Hi,
>
> On Sep 16, 2009, at 3:47 AM, Kishor Tappita wrote:
>
>> Dear List,
>>
>> I get the below error while trying to access biomaRt attributes.
>>
>>
>>> getBM(attributes = c("entrezgene"),values =
>>> c("202763_at","209310_s_at"),mart =ensembl)
>>
>> Error in getBM(attributes = c("entrezgene"), values = c("202763_at",
>> "209310_s_at"),  :
>> The query to the BioMart webservice returned an invalid result:
>> biomaRt expected a character string of length 1. Please report this to
>> the mailing list.
>
> Aren't you forgetting to pass in the "filters" parameter to the getBM
> function?
>
> It looks like you're trying to get an entrezgene id from some affy probe id?
> You have to tell the function what types of "things" you're passing into
> "values" using the "filter" param.
>
> Look closely (again) at the code in the Example section of ?getBM
>
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  |  Memorial Sloan-Kettering Cancer Center
>  |  Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
>