I attempted to retrieve values of dn and ds for human/mouse gene comparisons in Ensembl using BiomaRt (R application), and get the following error (with mart defined as ensembl human reference genome): t = getBM(attributes = "mmusculus_homolog_dn", filters = "hgnc_symbol", values = "GABRA6", mart = mart) Error in `[.data.frame`(result, , attributes) : undefined columns selected In contrast, if I try to retrieve some other attribute, such as mouse gene id, it works (e.g.) > t = getBM(attributes = "mmusculus_homolog_ensembl_gene", filters = "hgnc_symbol", values = "GABRA6", mart = mart) > t [1] "ENSMUSG00000020428" So it doesn't seem to be a syntax error. What am I doing wrong in calling the "mmmusculus...dn" attribute (and the same issue with ds)? Thanks very much, Marcus G. [[alternative HTML version deleted]]

Hi Marcus, You don't give sessionInfo(), so no idea if you have an outdated version or whatever. But this works for me. > mart <- useMart("ensembl","hsapiens_gene_ensembl") > getBM(c("mmusculus_homolog_dn","mmusculus_homolog_ds"), "hgnc_symbol", "GABRA6", mart) mmusculus_homolog_dn mmusculus_homolog_ds 1 0.0459 0.5686 > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] 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 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] 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_2.18.0 lattice_0.20-27 statmod_1.4.18 limma_3.18.13 loaded via a namespace (and not attached): [1] compiler_3.0.2 grid_3.0.2 RCurl_1.95-4.1 tools_3.0.2 XML_3.98-1.1 Best, Jim On Friday, March 14, 2014 1:40:12 PM, Marcus Goldberg wrote: > I attempted to retrieve values of dn and ds for human/mouse gene > comparisons in Ensembl using BiomaRt (R application), and get the following > error (with mart defined as ensembl human reference genome): > > t = getBM(attributes = "mmusculus_homolog_dn", filters = > "hgnc_symbol", values = "GABRA6", mart = mart) > Error in `[.data.frame`(result, , attributes) : > undefined columns selected > > In contrast, if I try to retrieve some other attribute, such as mouse gene > id, it works (e.g.) > >> t = getBM(attributes = "mmusculus_homolog_ensembl_gene", filters = "hgnc_symbol", values = "GABRA6", mart = mart) >> t > [1] "ENSMUSG00000020428" > > So it doesn't seem to be a syntax error. What am I doing wrong in calling > the "mmmusculus...dn" attribute (and the same issue with ds)? > > > Thanks very much, > > Marcus G. > > [[alternative HTML version deleted]] > > _______________________________________________ > 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