[BioC] getBM returns error
Wasco Wruck
wasco.wruck at charite.de
Thu Aug 11 16:17:50 CEST 2011
Hi Hans-Rudolf, Steffen, Johannes,
thank you for your answers and testing! I upgraded to the newest
versions but still got the same error. Using only one attribute to
useMart() I got a html error page which our network admin could
interpret - it was a not-easy-to-detect firewall problem concerning
HTTP1.1 expect!
Best wishes,
Wasco
Am 8/10/2011 6:48 PM, schrieb Hans-Rudolf Hotz:
> 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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>>>
>>>
>>
--
Wasco Wruck
Institute of Pathology
Charite Campus Mitte
Charite - Universitaetsmedizin Berlin
Chariteplatz 1
10117 Berlin
+49 30 450 536237
wasco.wruck at charite.de
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