[BioC] BiomaRt error: server down?

Wed Feb 22 12:33:06 CET 2012

Thank you Ekta,
This will do in the meantime.
Best, Lisa

On 22/02/12 11:27, Ekta Jain wrote:
> Hi Lisa,
> You can try doing the same from Ensembl bioMart http://www.ensembl.org/biomart/martview/c99651c657859e8078d6513f6b136815
> And selecting uniprot Swissport/TrEMBL under 'External'.
>
> -----Original Message-----
> From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Lisa Hopcroft
> Sent: 22 February 2012 16:52
> To: bioconductor at r-project.org
> Subject: [BioC] BiomaRt error: server down?
>
> Hallo,
>
> I'm trying to map Uniprot accessions to Ensembl protein IDs using the biomaRt library in bioconductor.  This has worked in the past, but I'm getting an error today.  Is the server down?  Is there anywhere/anyhow I can check whether the server is down?
>
> MWE and errors follow:
>
> =============================
> library(biomaRt)
>
> human.ensembl<- useMart("ensembl", dataset = "hsapiens_gene_ensembl") uniprot.list<- c( "Q09666" )
>
> uniprot2ensembl<- getBM(
>    attributes = c( "uniprot_swissprot_accession","ensembl_peptide_id" ),
>    filters    = "uniprot_swissprot_accession",
>    values     = uniprot.list,
>    mart       = human.ensembl )
>
> =============================
>                                                                                                                              V1
> 1<!DOCTYPE HTML PUBLIC -//W3C//DTD HTML 4.01 Transitional//EN http://www.w3.org/TR/html4/loose.dtd>
> 2<HTML><HEAD><META HTTP-EQUIV=Content-Type CONTENT=text/html; charset=iso-8859-1>
> 3<TITLE>ERROR: The requested URL could not be retrieved</TITLE>
> 4<STYLE type=text/css><!--BODY{background-color:#ffffff;font-family:verdana,sans-serif}PRE{font-family:sans-serif}--></STYLE>
> 5</HEAD><BODY>
> 6<H1>ERROR</H1>
> Error in getBM(attributes = c("uniprot_swissprot_accession", "ensembl_peptide_id"),  :
>    The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list.
> =============================
>
> Session info:
>
> R version 2.13.1 (2011-07-08)
> Platform: i686-pc-linux-gnu (32-bit)
>
> locale:
>   [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>   [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] biomaRt_2.8.1         preprocessCore_1.14.0 vsn_3.20.0            Biobase_2.12.2
>
> loaded via a namespace (and not attached):
> [1] affy_1.30.0     affyio_1.20.0   grid_2.13.1     lattice_0.19-33 limma_3.8.2     RCurl_1.91-1    tools_2.13.1
> [8] XML_3.9-4
>
>
> Many thanks in advance,
> Lisa
>
> PS. Apologies if I've sent this to the wrong place, please set me right if I have.
>
>
> --
>
> Dr Lisa Hopcroft (née McMillan)
> Postdoctoral research assistant
> www.dcs.gla.ac.uk/~lisa/<http://www.dcs.gla.ac.uk/~lisa/>
>
> R315 Level 3
> Paul O'Gorman Leukaemia Research Centre
> Gartnavel General Hospital
> Glasgow G12 0YN
> +44 (0) 141 301 7882
>
> R308 Level 3
> Sir Alwyn Williams Building
> School of Computing Science
> University of Glasgow
> Glasgow G12 8QQ
> +44 (0) 141 330 1648
>
> Skype: lisahopcroft
>
> [Working days: Tuesday-Friday]
>
>
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--

Dr Lisa Hopcroft (née McMillan)
Postdoctoral research assistant
www.dcs.gla.ac.uk/~lisa/

R315 Level 3
Paul O'Gorman Leukaemia Research Centre
Gartnavel General Hospital
Glasgow G12 0YN
+44 (0) 141 301 7882

R308 Level 3
Sir Alwyn Williams Building
School of Computing Science
University of Glasgow
Glasgow G12 8QQ
+44 (0) 141 330 1648

Skype: lisahopcroft

[Working days: Tuesday-Friday]

The University of Glasgow, charity number SC004401