Hello, This question isn't about profilePlots in particular, but about subsetting a vector by a set of values. > Top25Expr[which(annoT[,"symbol"]==as.character(peak[1,]) | annoT[,"symbol"]==as.character(peak[2,]) |annoT[,"symbol"]==as.character(peak[3,]) | annoT[,"symbol"]==as.character(peak[4,]) | annoT[,"symbol"]==as.character(peak[5,]) | annoT[,"symbol"]==as.character(peak[6,]) | annoT[,"symbol"]==as.character(peak[7,]) | annoT[,"symbol"]==as.character(peak[8,]) ............ )]<-TRUE One problem in your code is that you are comparing the symbol column with each row of peaks. Assuming that your peak table has a column called overlapsGene, which is the symbol of the gene that the peak overlaps, to do what you want in one line is : annoT[, "symbol"] %in% peak [, "overlapsGene"] This gives you a logical vector, each element being one of the genes in annoT. -------------------------------------- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia