Hi,
I've a bunch of files (20 samples divided in two groups: untreated vs treated). For each sample I've the global methylation BS and the "true" methylation oxBS, all files in .idat. So to compute the methylation profile I used ChAMP on the oxBS data. It worked well. Now in order to check for hydroxyMethylation (5-hmc) I've to substract the oxBS data from the BS data. Is it possible with ChAMP ?
Thanks