Dingxia, Please try this instead, TSS = getBM(c("gene", "chromosome_name", "chromosome_start", "chromosome_end", "chromosome_strand"), mart = mart) TSS = unique(TSS[!is.na(TSS[,3]),]) Annotation = RangedData(IRanges(start = as.numeric(TSS[, 3]), end = as.numeric(TSS[, 4]), names = as.character(TSS[, 1])), strand = TSS[, 5], space = as.character(TSS[, 2])) Best regards, Julie On 8/29/12 2:41 PM, "Dingxia Feng" <fengdxia@iastate.edu> wrote: Hi, Zhuli, I have to trouble to run the getAnnotation code. This is how I did it: > library(ChIPpeakAnno) > mart=useMart("WS220",dataset="wormbase_gene") > Annotation = getAnnotation(mart,featureType="TSS") Error in getBM(c("ensembl_gene_id", "chromosome_name", "start_position", : Invalid attribute(s): ensembl_gene_id, start_position, end_position, strand, description Please use the function 'listAttributes' to get valid attribute names So it looks the getAnnotation function recognize the ensemble database, not the WS220. The reason I need WS220 is that I used it in the previous alignment. So julie, is there a way to get this annotation work with WS220 in ChIPpeakAnno? Thanks. [[alternative HTML version deleted]]