Hi BioC, We are exploring if we could use 'charm' package for MeDIP (methyl-enrichment) arrays. The 'charm' package was designed for McrBC (methyl-depletion) arrays originally. We really like the normalization preprocessings, but in order to use for MeDIP, some modifications are required. According to the paper by Aryee et al Biostatistics 2011, 12:197-210. It seems that the normalization methods (within-sample, between-sample) are applicable to other tiling arrays regardless enrichment strategy. We agree with that. The paper defined log ratio mi = qi + ei where qi = -log(1-pi). pi represents proportion of methylated CpGs at a given locus i, ei is an error term. By this definition, larger qi represents more methylation in methyl-depleted arrays. However, for MeDIP, qi should be log(pi) instead of -log(1-pi). We are wondering if anyone here has also tried to modify the codes for MeDIP purpose? Any pointers? Is there any easy way to make the change? Regards, Johnny