[BioC] Biomart Error

[steffen at stat.Berkeley.EDU]

Hi Becky,

You query will work if you update biomaRt and use the developmental version.
You can download it from here:

http://bioconductor.org/packages/2.4/bioc/html/biomaRt.html

You also need to specify what filter you are using, this seem to be
missing in your query.

Once you've updated biomaRt try:

ensembl<-useMart("ensembl", dataset="hsapiens_gene_ensembl")

#use list filters to list the filternames
listFilters(ensembl)

#then do you query using the correct attribute and filter name

myGetBM <- getBM(attributes=c("refseq_dna_predicted","ensembl_gene_id"),
filter="refseq_dna_predicted",values=genes, mart=ensembl)

Cheers,
Steffen

> 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
>>
>> Fax No +44 (0) 207 269 3581
>>
>> <http://www.cancerresearchuk.org/>
>>
>>
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>
> Rhoda Kinsella Ph.D.
> Ensembl Bioinformatician,
> European Bioinformatics Institute (EMBL-EBI),
> Wellcome Trust Genome Campus,
> Hinxton
> Cambridge CB10 1SD,
> UK.
>
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