Dear Philip, I believe you can use biomaRt in R to convert ensembl ID to TAIR ID. source("http://bioconductor.org/biocLite.R") biocLite("biomaRt") ensembl = useMart("ensembl") listDatasets(ensembl) Once the dataset is identified, use the following example to select the dataset. hg = useDataset("hsapiens_gene_ensembl",mart=ensembl) The getBM function can be used to obtain both EnsemblIDs and TAIR IDs. I Cced the Bioconductor mailing list so that the biomaRt developers can chime in. Thanks! Kind regards, Julie On 7/16/10 3:50 PM, "pterry@huskers.unl.edu" <pterry@huskers.unl.edu> wrote: Dear Julie, Concerning your suggestion regarding "getEnrichedGO" and the Arabidopsis genome, annPeak = annotatePeakInBatch(rd_s8_ratio_gtr4[1:6, ], AnnotationData = Ann_arab) "... For now, I would suggest call getEnrichedGO function with a list of TAIR IDs using the following syntax. You need to first convert the list of Ensembl ID to TAIR ID first. enrichedGO.Arab <- getEnrichedGO (tarIDs, feature_id_type="entrez_id", orgAnn=""org.At.tair.db", maxP=0.05, multiAdj =TRUE, minGOterm=10, multiAdjMethod="BH") " I assume I need to convert Ensembl IDs in "annPeak" to TAIR IDs? I note 3 columns of these IDs in the "annPeak" RangedData object (only 2 when coerced to a dataframe). Can you recommend a way to convert these columns? I'm still learning Bioconductor. Thanks, Philip Terry pterry@huskers.unl.edu [[alternative HTML version deleted]]