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="" ~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]]
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@r-project.org [mailto:bioconductor-
bounces@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
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 (n?e 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]]
The information contained in this electronic message and in any
attachments to this message is confidential, legally privileged and
intended only for use by the person or entity to which this electronic
message is addressed. If you are not the intended recipient, and have
received this message in error, please notify the sender and system
manager by return email and delete the message and its attachments and
also you are hereby notified that any distribution, copying, review,
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transmission or the information contained in it is strictly
prohibited. Please note that any views or opinions presented in this
email are solely those of the author and may not represent those of
the Company or bind the Company. Any commitments made over e-mail are
not financially binding on the company unless accompanied or followed
by a valid purchase order. This message has been scanned for viruses
and dangerous content by Mail Scanner, and is believed to be clean.
The Company accepts no liability for any damage caused by any virus
transmitted by this email.
www.jubl.com
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.o
rg/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
> 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 (n?e 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]]
>
> The information contained in this electronic message and in any
attachments to this message is confidential, legally privileged and
intended only for use by the person or entity to which this electronic
message is addressed. If you are not the intended recipient, and have
received this message in error, please notify the sender and system
manager by return email and delete the message and its attachments and
also you are hereby notified that any distribution, copying, review,
retransmission, dissemination or other use of this electronic
transmission or the information contained in it is strictly
prohibited. Please note that any views or opinions presented in this
email are solely those of the author and may not represent those of
the Company or bind the Company. Any commitments made over e-mail are
not financially binding on the company unless accompanied or followed
by a valid purchase order. This message has been scanned for viruses
and dangerous content by Mail Scanner, and is believed to be clean.
The Company accepts no liability for any damage caused by any virus
transmitted by this email.
> www.jubl.com
>
--
Dr Lisa Hopcroft (n?e 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
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 (n?e 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]] > > The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. > www.jubl.com > -- Dr Lisa Hopcroft (n?e 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