Hello, I'm trying to use biomaRt to access SNP data from HapMap_rel27. > library(biomaRt) > hapmap<-useMart("HapMap_rel27") gives no trouble and I can list the available datasets. When I try to use any of the datasets I get the following: > hapmap<-useDataset("hm27_variation_ceu",mart=hapmap) Checking attributes ...Error in bmAttrFilt("attributes", mart) : biomaRt error: looks like we're connecting to incompatible version of BioMart suite. Can anyone suggest a work-around or error in what I'm doing? Or is it just not possible to access HapMap_rel27 with biomaRt? Session information included at the end of this message. Thanks, Brad --- Brad McNeney Statistics and Actuarial Science Simon Fraser University > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C [5] LC_TIME=English_Canada.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.4.0 loaded via a namespace (and not attached): [1] RCurl_1.4-2 tools_2.11.1 XML_3.1-0

Hi Brad, I recently fixed this and it should work using the devel version of biomaRt which you can get from here: http://www.bioconductor.org/packages/2.7/bioc/html/biomaRt.html Using that version I get the following: > hapmap<-useMart("HapMap_rel27") > hapmap<-useDataset("hm27_variation_ceu",mart=hapmap) > listFilters(hapmap) name description 1 allele_freq Minor Allele Frequency [>=] 2 center Genotyping Center 3 platform Genotyping Platform 4 monomorphic Monomorphic SNPs 5 marker_name List of HapMap SNPs 6 utr3 3' UTR 7 utr5 5' UTR 8 coding_synon Exons - synonymous coding SNPs 9 coding_nonsynon Exons - non-synonymous coding SNPs 10 intronic introns 11 chrom chromosome 12 start From position 13 stop To position 14 gene_list List of Genes 15 encode_region ENCODE region > sessionInfo() R version 2.10.0 (2009-10-26) i386-apple-darwin8.11.1 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.5.1 loaded via a namespace (and not attached): [1] RCurl_1.2-1 XML_2.6-0 Cheers, Steffen On Thu, Jun 24, 2010 at 3:40 PM, Brad McNeney <mcneney@gmail.com> wrote: > Hello, > > I'm trying to use biomaRt to access SNP data from HapMap_rel27. > > > library(biomaRt) > > hapmap<-useMart("HapMap_rel27") > > gives no trouble and I can list the available datasets. When I try to > use any of the datasets I get the following: > > > hapmap<-useDataset("hm27_variation_ceu",mart=hapmap) > Checking attributes ...Error in bmAttrFilt("attributes", mart) : > biomaRt error: looks like we're connecting to incompatible version > of BioMart suite. > > Can anyone suggest a work-around or error in what I'm doing? Or is it > just not possible to access HapMap_rel27 with biomaRt? > > Session information included at the end of this message. > > Thanks, > > Brad > --- > Brad McNeney > Statistics and Actuarial Science > Simon Fraser University > > > > sessionInfo() > R version 2.11.1 (2010-05-31) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 > [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C > [5] LC_TIME=English_Canada.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.4.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.4-2 tools_2.11.1 XML_3.1-0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]