[BioC] problems with biomaRt

Stefanie Carola Gerstberger scg74 at cornell.edu
Mon Feb 21 18:13:57 CET 2011


Hi, 
I'm having recently a problem with biomaRt in R.  I tried to access the human ensembl genes. I didn't have a problem until last week, but over the weekend I received this:

> > 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

Exactly this line happend for any kind of query, e.g. instead of hgnc_symbol I tried refseq_dna, ensembl_gene_id etc...

I contacted Ensembl and they suggested to go through the ensembl server by using 

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

however at command line :

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

I get : 


>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,
Stefanie


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