Hi, I wanted to get some exon information for specific genes. I wanted to use the hg17 build, since my SNP data is based on that. The code that I use is: ------------------------------------- library(biomaRt) entrezid <- "8334" martx <- "ensembl_mart_49" ensembl <- useMart(biomart=martx,dataset="hsapiens_gene_ensembl", archive=TRUE) ### "ensembl_mart_49" hg17 for wtccc zz <- getBM(attr = c("entrezgene","exon_stable_id", "exon_chrom_start","exon_chrom_end"), filters="with_entrezgene", values = entrezid,mart = ensembl) ------------------------------------ However, I get the following error: Error in listFilters(mart, what = "type") : The function argument 'what' contains an invalid value: type Valid are: name, description, options, fullDescription, filters5, filters6 I checked with listFilters(ensembl) and ?getBM, and the filters appear to be ok. What am I doing wrong? thanks! My sessionInfo(): R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: [1] GOstats_2.12.0 graph_1.24.1 Category_2.12.0 [4] GO.db_2.3.5 multtest_2.2.0 XML_2.6-0 [7] hgu133a.db_2.3.5 org.Hs.eg.db_2.3.6 RSQLite_0.7-3 [10] AnnotationDbi_1.8.0 GEOquery_2.8.0 RCurl_1.2-1 [13] bitops_1.0-4.1 biomaRt_2.2.0 DBI_0.2-4 [16] RColorBrewer_1.0-2 genefilter_1.28.0 affy_1.24.1 [19] Biobase_2.6.0 loaded via a namespace (and not attached): [1] affyio_1.14.0 annotate_1.24.0 [3] GSEABase_1.8.0 MASS_7.3-3 [5] preprocessCore_1.8.0 RBGL_1.20.0 [7] splines_2.10.0 survival_2.35-7 [9] tools_2.10.0 xtable_1.5-6 > [[alternative HTML version deleted]]

Hi Tim, biomaRt works with archives from about Ensembl version 52 and upwards. Hg17 corresponds to NCBI35 which is in Ensembl 35, you'll need to get a very old archive. You could get the data you need via the web BioMart interface: http://nov2005.archive.ensembl.org/index.html follow the BioMart link to make a query. Hope this helps, Steffen > Hi, > > I wanted to get some exon information for specific genes. I wanted to use > the hg17 build, since my SNP data is based on that. The code that I use > is: > ------------------------------------- > library(biomaRt) > entrezid <- "8334" > martx <- "ensembl_mart_49" > > ensembl <- useMart(biomart=martx,dataset="hsapiens_gene_ensembl", > archive=TRUE) ### "ensembl_mart_49" hg17 for wtccc > zz <- getBM(attr = c("entrezgene","exon_stable_id", > "exon_chrom_start","exon_chrom_end"), > filters="with_entrezgene", > values = entrezid,mart = ensembl) > > > ------------------------------------ > However, I get the following error: > Error in listFilters(mart, what = "type") : > The function argument 'what' contains an invalid value: type > Valid are: name, description, options, fullDescription, filters5, filters6 > > I checked with listFilters(ensembl) and ?getBM, and the filters appear to > be ok. What am I doing wrong? > thanks! > My sessionInfo(): > R version 2.10.0 (2009-10-26) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods > [7] base > > other attached packages: > [1] GOstats_2.12.0 graph_1.24.1 Category_2.12.0 > [4] GO.db_2.3.5 multtest_2.2.0 XML_2.6-0 > [7] hgu133a.db_2.3.5 org.Hs.eg.db_2.3.6 RSQLite_0.7-3 > [10] AnnotationDbi_1.8.0 GEOquery_2.8.0 RCurl_1.2-1 > [13] bitops_1.0-4.1 biomaRt_2.2.0 DBI_0.2-4 > [16] RColorBrewer_1.0-2 genefilter_1.28.0 affy_1.24.1 > [19] Biobase_2.6.0 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 annotate_1.24.0 > [3] GSEABase_1.8.0 MASS_7.3-3 > [5] preprocessCore_1.8.0 RBGL_1.20.0 > [7] splines_2.10.0 survival_2.35-7 > [9] tools_2.10.0 xtable_1.5-6 >> > > > > [[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 >