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
