Dear list,
With the help of friendly IT support, I have a solution to this
problem. I am posting their response here for anyone else
experiencing a similar problem.
Lisa
The biomaRt library calls the postForm function of RCurl to submit the
query to the web service. The resultant HTTP request contains an HTTP
1.1 header
Expect: 100 - continue
The squid proxy doesn't support HTTP 1.1. so responds with an error
"417: Expectation failed"
The RCurl manual suggested that the HTTP version can be restricted by
setting the http.version to the symbolic constant HTTP_VERSION_1_0
library(RCurl)
options(RCurlOptions =
list(proxy="wwwcache.gla.ac.uk:8080",http.version=HTTP_VERSION_1_0))
If I do this I can successfully retrieve the result for the example in
the help e.g.
library(RCurl)
options(RCurlOptions =
list(proxy="wwwcache.gla.ac.uk:8080",http.version=HTTP_VERSION_1_0))
library(biomaRt)
mart <- useMart("ensembl")
datasets <- listDatasets(mart)
mart<-useDataset("hsapiens_gene_ensembl",mart)
getBM(attributes=c("affy_hg_u95av2","hgnc_symbol","chromosome_name","b
and"),filters="affy_hg_u95av2",values=c("1939_at","1503_at","1454_at")
, mart=mart)
which results in the output
affy_hg_u95av2 hgnc_symbol chromosome_name band
1 1939_at TP53 17 p13.1
2 1503_at BRCA2 13 q13.1
3 1454_at SMAD3 15 q22.33
On 01/03/12 16:20, Steffen Durinck wrote:
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_
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>
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<mailto: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
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"></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
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"></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=""/><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<tel:%2b44%20%280%29%20141%20301%207882>
R308 Level 3
Sir Alwyn Williams Building
School of Computing Science
University of Glasgow
Glasgow G12 8QQ
+44 (0) 141 330 1648<tel:%2b44%20%280%29%20141%20330%201648>
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="" %7elisa=""/><http: 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<tel:%2b44%20%280%29%20141%20301%207882>
R308 Level 3
Sir Alwyn Williams Building
School of Computing Science
University of Glasgow
Glasgow G12 8QQ
+44 (0) 141 330 1648<tel:%2b44%20%280%29%20141%20330%201648>
Skype: lisahopcroft
[Working days: Tuesday-Friday]
________________________________
The University of Glasgow, charity number SC004401
[[alternative HTML version deleted]]
_______________________________________________
Bioconductor mailing list
Bioconductor@r-project.org<mailto:bioconductor@r-project.org>
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
--
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
[[alternative HTML version deleted]]
