Dear Joern, In the PLos paper, to find ChIP-enriched regions MAs data were "rbind" (MA <- do.call("rbind", MAs), and then find ChIP enriched regions based on smoothX using "findChersOnSmoothed". I am wondering if this function takes sample replicates into calculation. If not, how can I get the cher results based on mean values of replicates? Or the results with chers of each sample listed. So one can count chers out of the total number of replicates for each gene that was picked up by the method. Thanks, Jianping ################################## Jianping Jin Ph.D. Bioinformatics scientist Center for Bioinformatics Room 3133 Bioinformatics building CB# 7104 University of Chapel Hill Chapel Hill, NC 27599 Phone: (919)843-6105 FAX: (919)843-3103 E-Mail: jjin at email.unc.edu