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@upf.edu <mailto:martin.sikora@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@upf.edu <mailto:martin.sikora@upf.edu>

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