[BioC] problem with biomaRt

[James W. MacDonald]

Hi Stephanie,


On 2/21/2011 6:29 PM, Stefanie Carola Gerstberger wrote:
> 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)

I get

 > library(biomaRt)
 > mart <- useMart("ensembl","hsapiens_gene_ensembl")
 > getBM("ensembl_gene_id","hgnc_symbol", "FUS", mart)
   ensembl_gene_id
1 ENSG00000089280
 > sessionInfo()
R version 2.12.0 Patched (2010-11-23 r53652)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
  [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
  [5] LC_MONETARY=C                  LC_MESSAGES=en_US.iso885915
  [7] LC_PAPER=en_US.iso885915       LC_NAME=C
  [9] LC_ADDRESS=C                   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_2.6.0

loaded via a namespace (and not attached):
[1] RCurl_1.5-0 XML_3.2-0


What is the output of sessionInfo() for you?

Best,

Jim


>>
>
>> 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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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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