Hey, Has anyone ever used biomart to get the ENSEMBL ids for the Affymetrix rat exon array at the transcript cluster level: i.e. library(oligo) exonCELs <- list.celfiles("where the rat CEL files are", full.names=TRUE) affyExonFS <- read.celfiles(exonCELs) exonCore <- rma(affyExonFS, target = "core") # featureData(exonCore) <- getNetAffx(exonCore, "transcript") library(biomaRt) mart <- useMart("ensembl", dataset="rnorvegicus_gene_ensembl") genes <- getBM(attributes = c("ensembl_gene_id", "affy_raex_1_0_st_v1"), filters="affy_raex_1_0_st_v1", values=featureNames(exonCore), mart=mart) I do it but only get ensembl ids for a few of the transcripts. > dim(genes) [1] 370 2 > length(featureNames(exonCore)) [1] 8793 I don't understand this. In particular, I noticed any transcript id of 7xxxxxx would not return an ensembl id. I wondered if it might be that affy_raex_1_0_st_v1 summarises at the probeset or exon level, but in that case surely nothing would be returned by the getBM call? Any help would be much appreciated. I couldn't find an easy way to do the same thing using oligo / getNetAffx() but I may not have looked hard enough! My next option is to try xmapcore. Cheers, Jim > sessionInfo() R version 2.14.1 (2011-12-22) 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=C 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_2.10.0 pd.raex.1.0.st.v1_3.4.0 RSQLite_0.11.1 [4] DBI_0.2-5 oligo_1.18.1 oligoClasses_1.16.0 [7] Biobase_2.14.0 loaded via a namespace (and not attached): [1] affxparser_1.26.4 affyio_1.22.0 Biostrings_2.22.0 [4] bit_1.1-8 ff_2.2-5 IRanges_1.12.6 [7] preprocessCore_1.16.0 RCurl_1.91-1 splines_2.14.1 [10] XML_3.9-4 zlibbioc_1.0.1 -- James Perkins Institute of Structural and Molecular Biology Division of Biosciences University College London Gower Street London, WC1E 6BT UK email: j.perkins@ucl.ac.uk phone: 0207 679 2198 [[alternative HTML version deleted]]