[BioC] BiomaRt error: server down?
Hans-Rudolf Hotz
hrh at fmi.ch
Thu Mar 1 09:54:34 CET 2012
Hi Lisa
it works for me (see below).
I suggest you update to "R version 2.14.1" and "biomaRt_2.10.0" if you
still have problems check with you sysadmins for any recent changes in
your firewall settings.
Regards, Hans
> 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)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><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
>
>
> sessionInfo()R version 2.14.1 (2011-12-22)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.10.0
loaded via a namespace (and not attached):
[1] RCurl_1.9-5 XML_3.9-4
>
On 03/01/2012 09:40 AM, Lisa Hopcroft 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)
> <?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><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<!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("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<!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/%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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