[BioC] Biomart Error

Fri Mar 13 11:51:30 CET 2009

Hi Steffen,
I have fixed the internal name issue and this change has now been  
pushed to the live ensembl servers. If I do the following query it  
seems to work:

 > library(biomaRt)
 > mymart = useMart("ENSEMBL_MART_ENSEMBL",  
dataset="hsapiens_gene_ensembl", host="http://www.ensembl.org/biomart/martservice 
")
Checking attributes and filters ... ok
 > gene = c("XM_001124306")
 > getBM(attributes=c("refseq_dna_predicted", "ensembl_gene_id"),  
filters = "refseq_dna_predicted", values = gene, mart=mymart)
   refseq_dna_predicted ensembl_gene_id
1         XM_001124306 ENSG00000205358
 >

Hopefully it will therefore not be necessary for Becky to have to do  
an update.
Regards,
Rhoda

On 12 Mar 2009, at 22:20, steffen at stat.Berkeley.EDU wrote:

> 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
>>>
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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.
>>
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>>
>

Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.