Hi Steffen et al, Quick question about a search query via biomaRt. Here is the code that I am using: ***** library(biomaRt) ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") filters = listFilters(ensembl) attributes = listAttributes(ensembl) getBM(attributes=c("ensembl_peptide_id", "entrezgene", "ensembl_gene_id", "hgnc_automatic_gene_name"), filters="hgnc_automatic_gene_name", values="ATF4", mart=ensembl) ***** For me, this returns an empty data frame. But when I query ATF4 online at ensembl, I find what I need. I also looked up ATF4 at genenames.org (HUGO) and it seems that ATF4 is a valid hgnc gene name, so the filter so be fine. I guess the only other reason that I can see is which dataset I use in the useMart function. I am guessing that the online API will search through all datasets while I am only specifying a single one? If this is true, do you know of a sensible work around? I have about 150 genes that I would like mapped to the EBML ID names but using the code above with a vector of gene names, I can only map around 25...but if I manually query for some of the non-mapped gene names, I get what I am after. If I am wrong about my guess in the dataset, can you let me know what you think might be going on? Tony > sessionInfo() R version 2.11.0 Under development (unstable) (2010-01-16 r50993) i386-apple-darwin10.2.0 locale: [1] 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 [8] base other attached packages: [1] hgu133plus2.db_2.3.5 org.Hs.eg.db_2.3.6 Rgraphviz_1.25.1 [4] biomaRt_2.3.0 GOstats_2.13.0 RSQLite_0.8-1 [7] DBI_0.2-5 Category_2.13.0 AnnotationDbi_1.9.4 [10] Biobase_2.7.3 RBGL_1.23.0 graph_1.25.5 loaded via a namespace (and not attached): [1] annotate_1.25.1 genefilter_1.29.5 GO.db_2.3.5 GSEABase_1.9.0 [5] RCurl_1.3-1 splines_2.11.0 survival_2.35-8 tools_2.11.0 [9] XML_2.6-0 xtable_1.5-6 [[alternative HTML version deleted]]