Hi, I have EntrezGene IDs for which I want to retrieve dN and dS values from biomaRt. I've created the mart = "ensembl" for ensembl genes; chosen dataset = "hsapiens_gene_ensembl" for human genes; filter = "entrezgene"; attributes = c("entrezgene" "mmusculus_homolog_dn" "mmusculus_homolog_ds"). However, when I run getBM() with the above parameters I get the error below. Any ideas what could be wrong here? Thanks Gabriel Teku Lund University Faculty of Medicine Dept of Experimental Sciences Protein Structure and Bioinformatics Grp -- output of sessionInfo(): > mart = useMart("ensembl") > mart Object of class 'Mart': Using the ensembl BioMart database Using the dataset > ensembl <- useDataset(data ="hsapiens_gene_ensembl", mart = ensembl) > ensembl Object of class 'Mart': Using the ensembl BioMart database Using the hsapiens_gene_ensembl dataset > attrib = listAttributes(ensembl) > selected.attr <- attrib$name[grepl("(entrezgene|mmusculus_homolog_d)", attrib$name)] > selected.attr [1] "entrezgene" "mmusculus_homolog_dn" "mmusculus_homolog_ds" > filt = listFilters(ensembl) > selected.filt <- filt$name[ grepl("^entrezgene", filt$name)] > selected.filt [1] "entrezgene" > head(vs.c05) [1] "10000" "100" "10254" "10288" "10392" "10544" > head(vs.c05) #list of entrezgene ids [1] "10000" "100" "10254" "10288" "10392" "10544" > dn.ds <- getBM(selected.attr, selected.filt, values= vs.c05, ensembl ) Error in getBM(selected.attr, selected.filt, values = vs.c05, ensembl) : Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.14.0 seqinr_3.0-7 ape_3.0-7 loaded via a namespace (and not attached): [1] gee_4.13-18 grid_2.15.2 lattice_0.20-13 nlme_3.1-108 RCurl_1.95-3 tools_2.15.2 XML_3.95-0.1 -- Sent via the guest posting facility at bioconductor.org.

Hi Gabriel, On 2/19/2013 7:05 AM, Gabriel Teku [guest] wrote: > Hi, > > I have EntrezGene IDs for which I want to retrieve dN and dS values from biomaRt. > > I've created the mart = "ensembl" for ensembl genes; chosen dataset = "hsapiens_gene_ensembl" for human genes; filter = "entrezgene"; attributes = c("entrezgene" "mmusculus_homolog_dn" "mmusculus_homolog_ds"). > > However, when I run getBM() with the above parameters I get the error below. > > Any ideas what could be wrong here? Yes. If I take the error you got below, and go to the BioC website, click on mailing lists, and then paste into the search box, the second result from that search is https://stat.ethz.ch/pipermail/bioconductor/2010-May/033431.html Which I believe answers your question. Best, Jim > > Thanks > > Gabriel Teku > Lund University > Faculty of Medicine > Dept of Experimental Sciences > Protein Structure and Bioinformatics Grp > > -- output of sessionInfo(): > >> mart = useMart("ensembl") >> mart > Object of class 'Mart': > Using the ensembl BioMart database > Using the dataset >> ensembl<- useDataset(data ="hsapiens_gene_ensembl", mart = ensembl) >> ensembl > Object of class 'Mart': > Using the ensembl BioMart database > Using the hsapiens_gene_ensembl dataset >> attrib = listAttributes(ensembl) >> selected.attr<- attrib$name[grepl("(entrezgene|mmusculus_homolog_d)", attrib$name)] >> selected.attr > [1] "entrezgene" "mmusculus_homolog_dn" "mmusculus_homolog_ds" >> filt = listFilters(ensembl) >> selected.filt<- filt$name[ grepl("^entrezgene", filt$name)] >> selected.filt > [1] "entrezgene" >> head(vs.c05) > [1] "10000" "100" "10254" "10288" "10392" "10544" >> head(vs.c05) #list of entrezgene ids > [1] "10000" "100" "10254" "10288" "10392" "10544" >> dn.ds<- getBM(selected.attr, selected.filt, values= vs.c05, ensembl ) > Error in getBM(selected.attr, selected.filt, values = vs.c05, ensembl) : > Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed >> sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.14.0 seqinr_3.0-7 ape_3.0-7 > > loaded via a namespace (and not attached): > [1] gee_4.13-18 grid_2.15.2 lattice_0.20-13 nlme_3.1-108 RCurl_1.95-3 tools_2.15.2 XML_3.95-0.1 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099