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 <[email protected]> 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 > [email protected] > https://lists.biomart.org/mailman/listinfo/users > >
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