Hi Tejal, You'll need to do your query using the web interface at: http://aug2007.archive.ensembl.org/biomart/martview/ export as a tab delimited file and import that in R. Cheers, Steffen > Hi Steffen, > You are right, this version is too old, but I need to use the older > version. > Any suggestions ? > > -Tejal > > On Wed, Nov 11, 2009 at 5:49 PM, <steffen at="" stat.berkeley.edu=""> wrote: > >> Hi Tejal, >> >> Ensembl 46 is to old and there have been some major changes since for >> biomaRt to work with it. Would a more recent ensembl archive work for >> you? >> For example Ensembl 54 is NCBI36 and might be what you were looking for >> unless you have another reason to specifically want Ensembl 46? >> You can access Ensembl 54 like this: >> >> > listMarts(host="may2009.archive.ensembl.org/biomart/martservice") >> biomart version >> 1 ENSEMBL_MART_ENSEMBL Ensembl 54 >> 2 ENSEMBL_MART_SNP Ensembl Variation 54 >> 3 ENSEMBL_MART_VEGA Vega 35 >> 4 REACTOME Reactome(CSHL US) >> 5 wormbase_current WormBase (CSHL US) >> 6 pride PRIDE (EBI UK) >> > ens54 = useMart("ENSEMBL_MART_ENSEMBL", >> dataset="hsapiens_gene_ensembl" >> ,host="may2009.archive.ensembl.org/biomart/martservice") >> Checking attributes and filters ... ok >> >> >> >> Cheers, >> Steffen >> >> >> >> > Hi, >> > I have been trying to work with an archived version of ensembl mart, >> i.e. >> > ensembl_46. The code goes as follow: >> > >> >>library(biomaRt) >> >>#listMarts(archive=TRUE) >> >>mart=useMart("ensembl_mart_46", archive=TRUE) >> >>## listDatasets(mart) >> >>mart=useDataset("mmusculus_gene_ensembl",mart) >> > Checking attributes ... ok >> > Checking filters ... ok >> > Warning messages: >> > 1: In bmAttrFilt("attributes", mart) : >> > biomaRt warning: looks like we're connecting to an older version of >> > BioMart suite. Some biomaRt functions might not work. >> > 2: In bmAttrFilt("filters", mart) : >> > biomaRt warning: looks like we're connecting to an older version of >> > BioMart suite. Some biomaRt functions might not work. >> > >> >> plusStrand = new("GeneRegion", chromosome = "17", start = 30450000, >> end >> >> = >> > 30550000, strand = "+", biomart = mart) >> > >> > >> > I have modified the GeneRegion method such that it can work with >> older, >> > hardcoded attribute names. It started to give error once again due to >> > "strand" not being one of the filters supported by old ensembl build. >> > Therefore, I tried a simpler way to collect genomic features from >> biomart >> > : >> > >> > > getBM(c("gene_stable_id","transcript_stable_id", >> > >> > "exon_stable_id","exon_chrom_start","exon_chrom_end", >> > "rank", >> > "transcript_chrom_strand","struct_biotype"), >> > >> > >> filters=c("chromosome_name","start","end"),values=list(17,30450000, 30455000),mart) >> > >> > Error in listFilters(mart, what = "type") : >> > The function argument 'what' contains an invalid value: type >> > Valid are: name, description, options, fullDescription >> > >> > I also tried out with listFilters function : >> > listFilters("chromosome_name",mart=mart), which results in the same >> error. >> > >> > What is going on here, and how can I rectify it ? >> > >> > Here is my session info: >> > >> > R version 2.9.1 (2009-06-26) >> > i386-apple-darwin8.11.1 >> > >> > locale: >> > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> > >> > attached base packages: >> > [1] grid stats graphics grDevices utils datasets >> methods >> > base >> > >> > other attached packages: >> > [1] GenomeGraphs_1.0.1 biomaRt_2.0.0 >> > >> > loaded via a namespace (and not attached): >> > [1] RCurl_0.94-1 XML_2.6-0 >> > >> > >> > Thanks, >> > Tejal >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at stat.math.ethz.ch >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> >> >