Ok the error has now been fixed as of version 2.3.1. Regarding MEDIP data, i have never tried to use the charm pipeline on MEDIP data, though you might still get it to work. You may want to try changing getM to define l as logit(methyl-enriched/untreated), and you may need to use l instead of p in dmrFinder if that's the function you're using. Good luck. peter [[alternative HTML version deleted]]