I'm using MEDIPS to process MBD-seq data, with 2 control replicates and 3 case replicates. It seems that the MEDIPS.meth function needs same length of MSet (I got error message 'MEDIPSset/MEDIPSroiSet objects are of different length'). Any advice for this issue? I can use the MEDIPS.mergeSets, but this will make the replicates into one.
Thanks in advance,