On Fri, Sep 30, 2011 at 2:51 PM, Steffen Durinck <sdurinck@gmail.com> wrote:

> Hi RIchard, Arek,
>
> If you set verbose=TRUE in your getBM query you'll see the XML query that
> is send to the BioMart server (see below for your example).
> The order of the attributes in the XML query is usually the same order we
> get the results back from the BioMart server.
> However for your example this is not the case and there is no way for
> biomaRt to know this (Arek correct me if this is not the case), so when we
> add column names to the returned matrix they will be wrong when the query
> order is not preserved in the returned result.
>
> > multiTest = getBM(attributes= c("organism_name", "transcript_name",
> "exon_chrom_start", "exon_chrom_end"), filters="orgid", values="167",
> mart=phyto,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 =
> 'phytozome'><Attribute name = 'organism_name'/><Attribute name =
> 'transcript_name'/><Attribute name = 'exon_chrom_start'/><Attribute name =
> 'exon_chrom_end'/><Filter name = 'orgid' value = '167' /></Dataset></Query>
>
>
Okay, I see that on my end as well. Is this a consequence of biomart v0.6 on
the backend that would be alleviated by our plans to upgrade to 0.7 soon?


>
> Cheers,
> Steffen
>
>
> On Thu, Sep 29, 2011 at 9:08 AM, Arek Kasprzyk <arek.kasprzyk@gmail.com>wrote:
>
>> Hi Richard,
>> the best person to help you is Steffen Durinck, the original biomaRt coder
>> (cc'ed on this email)
>>
>> a
>>
>> On Wed, Sep 28, 2011 at 3:52 PM, Richard Hayes <rdhayes@lbl.gov> wrote:
>>
>>> Hi,
>>>
>>> Our group maintains the biomart instance at the Phytozome plant genomics
>>> portal. We've had some users report problems with the result sets from the
>>> biomaRt interface. It is unclear if this is a biomaRt problem or a problem
>>> in our mart configuration. At the moment, we are still running biomart
>>> version 0.6, but are hoping to upgrade in the very near future to 0.7.
>>>
>>> I had been testing with R 2.12.2 and biomaRt 2.6.0, but then upgraded to
>>> R 2.13.1 and biomaRt 2.8.1. The problems persist with these latest software
>>> releases.
>>>
>>> I can successfully connect to our mart and the main genome transcript
>>> dataset as follows, successfully retrieving a single column of transcript
>>> names for Arabidopsis thaliana using our internal "orgid" filter for
>>> organism ID 167:
>>>
>>> > library('biomaRt')
>>> > phyto=useMart('phytozome_mart', dataset='phytozome')
>>> > transcripts = getBM(attributes = c("transcript_name"), filters=
>>> "orgid", values="167", mart=phyto)
>>> > transcripts[1:5,]
>>> [1] "AT2G38230.1" "AT2G39920.2" "AT2G26530.1" "AT2G28630.1" "AT2G19280.1"
>>>
>>> However, when I construct a multicolumn query, the columns are not
>>> returned in the expected order:
>>>
>>> > multiTest = getBM(attributes= c("organism_name", "transcript_name",
>>> "exon_chrom_start", "exon_chrom_end"), filters="orgid", values="167",
>>> mart=phyto)
>>> > multiTest[1:5,]
>>>   organism_name transcript_name exon_chrom_start exon_chrom_end
>>> 1   AT5G47220.1        19171862         19172823      Athaliana
>>> 2   AT1G71920.3        27067059         27067098      Athaliana
>>> 3   AT1G71920.3        27067189         27067401      Athaliana
>>> 4   AT1G71920.3        27067506         27067589      Athaliana
>>> 5   AT1G71920.3        27067706         27067860      Athaliana
>>>
>>> Any help diagnosing the source of this problem is much appreciated.
>>>
>>> Best regards,
>>>
>>> --
>>> Richard D. Hayes, Ph.D.
>>> Joint Genome Institute / Lawrence Berkeley National Lab
>>> http://www.phytozome.net
>>>
>>> _______________________________________________
>>> Users mailing list
>>> Users@biomart.org
>>> https://lists.biomart.org/mailman/listinfo/users
>>>
>>>
>>
>


-- 
Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net

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