Hi Lisa,
This query works for me, maybe the BioMart server was temporarily down
at
the time you tried the query:
>
getBM(attributes=c("affy_hg_u95av2","hgnc_symbol"),filters="affy_hg_u9
5av2",values=c("1939_at"),
mart=human.ensembl,verbose=TRUE)
<query virtualschemaname="default" uniquerows="1" count="0" datasetconfigversion="0.6" requestid="biomaRt"> <dataset name="hsapiens_gene_ensembl"><attribute name="affy_hg_u95av2"/><attribute name="hgnc_symbol"/><filter name="affy_hg_u95av2" value="1939_at"/></dataset></query>
affy_hg_u95av2 hgnc_symbol
1 1939_at TP53
Cheers,
Steffen
On Thu, Mar 1, 2012 at 12:40 AM, Lisa Hopcroft
<lisa.hopcroft@glasgow.ac.uk>wrote:
> Hi,
>
> I'm still getting the error that I described in my previous email.
I'm
> now wanting to use biomaRt for something else and I really don't
want to
> have to use a flatfile format.
>
> Is everyone getting this error? (MWE to follow at end of email).
>
> Is the server down? Does anyone know how to check whether the
server is
> down?
>
> Thanks again,
> Lisa
>
> MWE (modified from getBM help file):
>
>
> > rm(list=ls())
> > library(biomaRt)
> > mart <- useMart("ensembl")
> > human.ensembl <-useDataset("hsapiens_gene_ensembl",mart)
> >
> getBM(attributes=c("affy_hg_u95av2","hgnc_symbol"),filters="affy_hg_
u95av2",values=c("1939_at"),
> mart=human.ensembl,verbose=TRUE)
> <query> virtualSchemaName = 'default' uniqueRows = '1' count = '0'
> datasetConfigVersion = '0.6' requestid= "biomaRt"> <dataset name=""> 'hsapiens_gene_ensembl'><attribute name="affy_hg_u95av2"/><attribute name=""> = 'hgnc_symbol'/><filter name="affy_hg_u95av2" value="1939_at"> /></dataset></query>
>
> V1
> 1 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
>
ERROR: The requested URL could not be retrieved
> 4 <style> type=text/css></style>
> 5
> </head><body>
> 6
>
ERROR
> Error in getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol"),
filters =
> "affy_hg_u95av2", :
> 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.
>
> > sessionInfo()
> 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 LC_MONETARY=C
> [6] LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C
> LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid stats graphics grDevices utils datasets
methods
> base
>
> other attached packages:
> [1] biomaRt_2.8.1 limma_3.8.2 gplots_2.8.0 caTools_1.12
> bitops_1.0-4.1 gtools_2.6.2 gdata_2.8.2
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.91-1 tools_2.13.1 XML_3.9-4
> >
>
>
>
> On 22/02/12 11:22, Lisa Hopcroft wrote:
> 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 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
>
ERROR: The requested URL could not be retrieved
> 4 <style> type=text/css></style>
> 5
> </head><body>
> 6
>
ERROR
> 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="" %7elisa=""/>
>
> 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]
>
>
>
> --
>
> 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]
>
>
> ________________________________
> The University of Glasgow, charity number SC004401
>
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>
>
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