Hi Laurent, No there is no update on this issue. Unless the BioMart server can return column headers, the biomaRt package can not know in which order the query results come back and assumes it is in the same order as the attributes specified in the query (which it does for most of the queries). Arek, let me know if you have any solution to this.
Cheers, Steffen On Wed, Oct 19, 2011 at 6:52 AM, Laurent Gatto <[email protected]>wrote: > Dear all, > > Any update about the column order in biomaRt results? > I have come across the same issue, as illustrated below. > > > library(biomaRt) > > mart = useMart("plants_mart_10","athaliana_eg_gene") > > ans <- getBM(attributes=c("tair_locus","peptide"), filter="tair_locus", > value=c("AT3G18780","AT2G26300"), mart=mart, 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 = > 'athaliana_eg_gene'><Attribute name = 'tair_locus'/><Attribute name = > 'peptide'/><Filter name = 'tair_locus' value = 'AT3G18780,AT2G26300' > /></Dataset></Query> > > ans > > > > > tair_locus > 1 MAEADDI[...]ASLIDQILFRILLHAN* > 2 MGLLCSR[...]VKKRRRNLLEAGLL* > 3 MAEADDI[...]ILASAGPGIVHRKCF* > peptide > 1 AT3G18780 > 2 AT2G26300 > 3 AT3G18780 > > I see the same for useMart("ensembl","ensembl_gene_id") using > ensembl_gene_id or ensembl_exon_id as filters. > In these cases, datasetConfigVersion is also 0.6, if that's of any help. > > > sessionInfo() > R Under development (unstable) (2011-10-13 r57241) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C > [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 > [5] LC_MONETARY=en_GB.utf8 LC_MESSAGES=en_GB.utf8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.9.3 > > loaded via a namespace (and not attached): > [1] RCurl_1.6-10 XML_3.4-3 > > Best wishes, > > Laurent > > On 30 September 2011 23:11, Richard Hayes <[email protected]> wrote: > > On Fri, Sep 30, 2011 at 2:51 PM, Steffen Durinck <[email protected]> > 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 <[email protected] > >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 <[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 > >>>> > >>>> > >>> > >> > > > > > > -- > > Richard D. Hayes, Ph.D. > > Joint Genome Institute / Lawrence Berkeley National Lab > > http://www.phytozome.net > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > [email protected] > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > [ Laurent Gatto | slashhome.be ] > > _______________________________________________ > Bioconductor mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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