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
>
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>
>

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