[BioC] biomart package - error querying for ensembl gene ID in snp mart

[Rhoda Kinsella]

Apologies if you have already received this message. I had a bounce  
back message from the
Bioconductor mailing list so I thought I should re-send, just in case...


Hi Martin,
I have looked into this and I can't seem to reproduce the error using  
the webservice (see screenshot).
Can you send me a screen shot of the mart web interface query that you  
performed along with the
error that you get from the web interface?
Regards,
Rhoda

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On 24 Feb 2009, at 22:33, martin sikora wrote:

> ok, so i seem to get the same error on the biomart web-service, so
> definitely some problem of the database..
>
> thanks anyways,
>
> cheers
> martin
>
> martin sikora schrieb:
>> dear all,
>>
>> i am getting an error trying to retrieve some attributes from the
>> variation biomart at ensembl (see code below). so far i got this  
>> error
>> only when trying to retrieve either ensembl gene or transcript IDs  
>> for
>> a certain SNP. other queries like alleles etc seem to work fine.  
>> maybe
>> some changes at the biomart server for these attributes?
>>
>> cheers
>> martin
>>
>> ---
>>
>>> library( biomaRt )
>>> snp129Mart <- useMart( "snp", dataset = "hsapiens_snp" )
>> Checking attributes and filters ... ok
>>> getBM( attributes = c( "ensembl_gene_stable_id"), filter = "refsnp",
>> "rs10399749", mart = snp129Mart )
>>
>> ensembl_gene_stable_id
>> 1 Query ERROR: caught BioMart::Exception::Database: Error during  
>> query
>> execution: File
>> './snp_mart_52/hsapiens_snp__transcript_variation__dm.MYD' not found
>> (Errcode: 27)
>>
>>
>>> sessionInfo()
>>
>> R version 2.8.1 Patched (2009-01-19 r47650)
>> i386-apple-darwin9.6.0
>>
>> locale:
>> C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices datasets  utils     methods   base
>>
>> other attached packages:
>> [1] biomaRt_1.16.0    R.utils_1.1.1     R.oo_1.4.6
>> R.methodsS3_1.0.3
>>
>> loaded via a namespace (and not attached):
>> [1] RCurl_0.94-1 XML_2.1-0    tools_2.8.1
>>
>>
>> -- 
>> :: martin sikora
>> :: IBE, institut de biologia evolutiva (UPF-CSIC)
>> :: CEXS-UPF-PRBB
>> :: doctor aiguader 88, 08003 barcelona
>>
>> :: tel. (+34) 93 316 0802
>> :: martin.sikora at upf.edu <mailto:martin.sikora at upf.edu>
>
>
> -- 
> :: martin sikora
> :: IBE, institut de biologia evolutiva (UPF-CSIC)
> :: CEXS-UPF-PRBB
> :: doctor aiguader 88, 08003 barcelona
>
> :: tel. (+34) 93 316 0802
> :: martin.sikora at upf.edu <mailto:martin.sikora at upf.edu>
>
> 	[[alternative HTML version deleted]]
>
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.