[BioC] problem with biomaRt

Stefanie Carola Gerstberger scg74 at cornell.edu
Tue Feb 22 00:29:16 CET 2011


Hi all, 
I frequently use R biomaRt for querying ensembl. Over the weekend I experienced a problem with biomaRt. whatever I query I get 

> library(biomaRt)
> ensembl=useMart("ensembl")
> listDatasets(ensembl)
> ens_sap=useMart("ensembl", dataset="hsapiens_gene_ensembl")
> attr_sap=listAttributes(ens_sap)
> filter_sap=listFilters(ens_sap)
> 

> getBM(attributes="ensembl_gene_id", filters="hgnc_symbol", values="FUS", 
>mart=ens_sap)

Error in getBM(attributes = "ensembl_gene_id", filters = "hgnc_symbol",  : 
  Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql 
database ensembl_mart_61: DBI 
connect('database=ensembl_mart_61;host=dcc-qa-db.oicr.on.ca;port=3306','bm_web',...)
failed: Can't connect to MySQL server on 'dcc-qa-db.oicr.on.ca' (113) at 
/srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm
line 98

> getBM(attributes="ensembl_gene_id", filters="refseq_dna", 
>values="NM_001134363", mart=ens_sap)


I asked ensembl help desk and they advised me to use directly ensembl mart through this:

>library(biomaRt)
>ensembl=useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
>dataset="hsapiens_gene_ensembl"
>ensembl=useDataset(dataset, mart=ensembl)

..however when I try this command I get the following:

> ensembl=useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")


Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing


Does anyone know how to fix this problem?

Thanks a lot,
Stefanie



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