[BioC] getBM returns error

Wed Aug 10 18:48:57 CEST 2011

Hi Wasco

well, it works for me as well (using R 2.13.1 and biomaRt_2.8.1), see below.

I suggest to upgrade, most likely your  R  2.11.0 and biomaRt_2.4.0 
doesn't work with the Biomart database from ensembl 63 (which was 
released a few weeks ago)....on the other hand the error message you 
provide: "Die angeforderte URL konnte nicht gefunden werden" does sound 
like a firewall problem on your side......

Regards, Hans

 > library("biomaRt")
 > mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
 > o=getBM(c("ensembl_gene_id", "ensembl_transcript_id",
+     "illumina_humanwg_6_v2"), mart=mart)
 >  head(o)
   ensembl_gene_id ensembl_transcript_id illumina_humanwg_6_v2
1 ENSG00000203347       ENST00000366172
2 ENSG00000256017       ENST00000379355          ILMN_1676712
3 ENSG00000236057       ENST00000537266
4 ENSG00000236057       ENST00000446137
5 ENSG00000245602       ENST00000500835
6 ENSG00000247217       ENST00000499475
 > sessionInfo()
R version 2.13.1 (2011-07-08)
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=C              LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       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_2.8.1

loaded via a namespace (and not attached):
[1] RCurl_1.6-6 XML_3.4-0
 >

On 08/10/2011 06:00 PM, Wasco Wruck wrote:
> Hi Steffen , hi Johannes,
>
> I consistently get the same error. Something must have changed because
> before some days it worked fine. Maybe I have to update.
>
> Wasco
>
> Am 8/10/2011 5:17 PM, schrieb Steffen Durinck:
>> Hi Wasco,
>>
>> This works for me, maybe the server was temporarily down, any chance
>> you can try again?
>>
>> Steffen
>>
>> On Wed, Aug 10, 2011 at 5:16 AM, Wasco Wruck<wasco.wruck at charite.de
>> <mailto:wasco.wruck at charite.de>>  wrote:
>>
>>      Hi,
>>
>>      I am getting an error for a biomaRt getBM() call which used to
>>      work before. Has something changed in getBM() or the corresponding
>>      web services - or might there be firewall problems? I have the
>>      environment variable http_proxy set and other commands through the
>>      firewall, e.g. package installations work. Also getting the same
>>      information from biomart via wget and a xml query works through
>>      http_proxy. Here is the output:
>>
>>      >  library("biomaRt")
>>      >  mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
>>      Checking attributes ... ok
>>      Checking filters ... ok
>>      >  o=getBM(c("ensembl_gene_id", "ensembl_transcript_id",
>>      "illumina_humanwg_6_v2"), mart=mart)
>>
>>
>>
>>
>>                  V1
>>      1<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN"
>>      "http://www.w3.org/TR/html4/strict.dtd">  <html><head>  <meta
>>      http-equiv="Content-Type" content="text/html;<title>FEHLER: Die
>>      angeforderte URL konnte nicht gefunden werden</title>  <style
>>      type="text/css"><!--   /*
>>      2
>>
>>
>>                                                       Stylesheet for
>>      Squid Error pages
>>      3
>>
>>
>>                                              Adapted from design by
>>      Free CSS Templates
>>      4 http://www.freecsstemplates.org
>>      5
>>
>>
>>                     Released for free under a Creative Commons
>>      Attribution 2.5 License
>>      6
>>
>>
>>
>>                   */
>>      Fehler in getBM(c("ensembl_gene_id", "ensembl_transcript_id",
>>      "illumina_humanwg_6_v2"),  :
>>       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 2.11.0 (2010-04-22)
>>      x86_64-unknown-linux-gnu
>>
>>      locale:
>>       [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C
>>       [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8
>>       [5] LC_MONETARY=C              LC_MESSAGES=de_DE.UTF-8
>>       [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C
>>       [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>      [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
>>
>>      attached base packages:
>>      [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>>      other attached packages:
>>      [1] biomaRt_2.4.0
>>
>>      loaded via a namespace (and not attached):
>>      [1] RCurl_1.4-1 XML_2.8-1
>>
>>
>>      Best regards,
>>      Wasco
>>
>>      --
>>
>>      Wasco Wruck
>>      Institute of Pathology
>>      Charite Campus Mitte
>>      Charite - Universitaetsmedizin Berlin
>>      Chariteplatz 1
>>      10117 Berlin
>>      +49 30 450 536237<tel:%2B49%2030%20450%20536237>
>>      wasco.wruck at charite.de<mailto:wasco.wruck at charite.de>
>>
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>>
>>
>
>