[BioC] Biomart Error

[Rhoda Kinsella]

Hi Becky,
I have had a look at the Ensembl mart configuration and there are  
differences between the internal_name for the refseq dna predicted  
filter and attribute names. One has lowercase "dna" and the other has  
uppercase "DNA". I am in the process of fixing this and will let you  
know when it has been solved. Many thanks for reporting the bug and  
apologies for any inconvenience.
Regards,
Rhoda


On 10 Mar 2009, at 16:26, Becky Saunders wrote:

> Hi There,
>
> I have an error on Biomart where I can not use the  
> refseq_dna_predicted
> attribute.
>
> If I use the following gene id data and the following commands I get  
> the
> error:
>
>> genes
>             V1
> 1  XM_001000131
> 2  XM_001001115
> 3  XM_001001128
> 4  XM_001001137
> 5  XM_001002091
> 6  XM_001005165
> 7  XM_001005681
> 8  XM_001005979
> 9  XM_001006801
> 10 XM_001123368
> 11 XM_001123369
> 12 XM_001123374
> 13 XM_001123393
> 14 XM_001123395
> 15 XM_001123428
> 16 XM_001123478
> 17 XM_001124305
> 18 XM_001124623
> 19 XM_001124624
> 20 XM_001124630
> 21 XM_001124642
> 22 XM_001124651
>
>> mart = useMart("ensembl")
>> ensembl<-useDataset("hsapiens_gene_ensembl", mart=mart)
> Checking attributes and filters ... ok
>> myGetBM <- getBM(attributes=c("refseq_DNA_predicted",
> "ensembl_gene_id"), values=genes, mart=ensembl)
>
> V1
> 1 Query ERROR: caught BioMart::Exception::Usage: Attribute
> refseq_DNA_predicted NOT FOUND
> Error in getBM(attributes = c("refseq_DNA_predicted",
> "ensembl_gene_id"),  :
>  Number of columns in the query result doesn't equal number of
> attributes in query.  This is probably an internal error, please  
> report.
>>
>
>
> Can anyone help? Basically I am just trying to map ensembl ids to both
> XM_ and NM_ RefSeq IDs.
>
> Many Thanks,
>
> Becky
>
> --
>
> Dr Rebecca Saunders
>
> High Throughput Screening Laboratory - Cancer Research UK
>
> Tel No. +44 (0)207 269 3159
>
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>
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.