Dear all, I am trying to use the charm package to analyze a Human 2.1M Deluxe Promoter Array dataset produced using the MeDIP protocol (i.e. untreated sample on one channel and enriched for methylated DNA from same sample on the other channel, [unlike the McrBC protocol used to illustrate the use of charm where the treated sample is enriched for unmethylated DNA]). Although the "Human 2.1M Deluxe Promoter Array (pd.081229.hg18.promoter.medip.hx1)" is being supported by the charm packge, I did not see anywhere how one specifies the type of protocol used (MEDIP vs McrBC). It appears to me that the methylation estimate would just change meaning from (0=unmethylated; 1=methylated) to (1=unmethylated; 0=methylated) if MeDIP arrays are used instead of McrBC arrays in chram but any suggestions would be appreciated. Thanks, Adi Tarca