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

[martin sikora]

hi rhoda,

thanks for the reply! i have found out that this error does only occur 
when you use the central biomart server, directly at ensembl it works, 
as you have shown. you can see the error in the screenshots, the one 
without Ensembl Gene ID works fine, but once i add it i get the same 
error as with using the biomaRt package. is there a way to use the 
ensembl server instead in the package?

cheers
martin

Rhoda Kinsella schrieb:
> 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
>
>
> ------------------------------------------------------------------------
>
>
>
>
> 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.
>


-- 
:: 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>
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