[BioC] BiomaRt error

[Aedin Culhane]

Thanks Steffen
Aedin

Steffen at stat.Berkeley.EDU wrote:
> It looks like the central repository at www.biomart.org doesn't work at the
> moment.  This is what biomaRt uses as default server.
>
> You could reroute and use www.ensembl.org as webservice until the central
> service is fixed. Below an example to reroute:
>
>
>   
>> listMarts(host="www.ensembl.org")
>>     
>                biomart                        version
> 1 ENSEMBL_MART_ENSEMBL                     Ensembl 55
> 2     ENSEMBL_MART_SNP           Ensembl variation 55
> 3 ENSEMBL_MART_FUNCGEN Ensembl functional genomics 55
> 4    ENSEMBL_MART_VEGA                        Vega 35
> 5             REACTOME            Reactome (CSHL US)
> 6     wormbase_current             WormBase (CSHL US)
> 7                pride                 PRIDE (EBI UK)
>   
>> mart =
>>     
> useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl",host="www.ensembl.org")
> Checking attributes ... ok
> Checking filters ... ok
>
>
> Once you're connected you via www.ensembl.org you should be able to do
> your queries.
>
> Cheers,
> Steffen
>
>   
>> I am getting a biomaRt error. it works last night, but is failing today.
>>
>>  > library(biomaRt)
>>  > example(getBM)
>>
>> getBM> if(interactive()){
>> getBM+ mart <- useMart("ensembl")
>> getBM+ datasets <- listDatasets(mart)
>> getBM+ mart<-useDataset("hsapiens_gene_ensembl",mart)
>> getBM+
>> getBM(attributes=c("affy_hg_u95av2","hgnc_symbol","chromosome_name","band"),filters="affy_hg_u95av2",values=c("1939_at","1503_at","1454_at"),
>> mart=mart)
>> getBM+
>> getBM+ }
>> Checking attributes and filters ... ok
>>
>> V1
>> 1 Query ERROR: caught BioMart::Exception::Database: Error during query
>> execution: Can't find file:
>> './ensembl_mart_55/hsapiens_gene_ensembl__ox_AFFY_HG_U95Av2__dm.frm'
>> (errno: 13)
>> Error in getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol",
>> "chromosome_name",  :
>>   Number of columns in the query result doesn't equal number of
>> attributes in query.  This is probably an internal error, please report.
>>
>>  > sessionInfo()
>> R version 2.9.0 (2009-04-17)
>> i486-pc-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] biomaRt_1.16.0
>>
>> loaded via a namespace (and not attached):
>> [1] RCurl_0.94-1 XML_1.93-2
>>
>> --
>> Aedín Culhane,
>> Research Associate
>> Computational Biology and Functional Genomics Laboratory
>> Harvard School of Public Health, Dana-Farber Cancer Institute
>>
>> 44 Binney Street, SM822C
>> Department of Biostatistics and Computational Biology,
>> Dana-Farber Cancer Institute
>> Boston, MA 02115
>> USA
>>
>> Phone: +1 (617) 632 2468
>> Fax:   +1 (617) 582 7760
>> Email: aedin at jimmy.harvard.edu
>> Web URL: http://www.hsph.harvard.edu/research/aedin-culhane/
>>
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>>
>>     
>
>   


-- 
Aedín Culhane,
Research Associate
Computational Biology and Functional Genomics Laboratory
Harvard School of Public Health, Dana-Farber Cancer Institute

44 Binney Street, SM822C
Department of Biostatistics and Computational Biology,
Dana-Farber Cancer Institute
Boston, MA 02115
USA

Phone: +1 (617) 632 2468
Fax:   +1 (617) 582 7760
Email: aedin at jimmy.harvard.edu
Web URL: http://www.hsph.harvard.edu/research/aedin-culhane/