I am using NimbleGen 3x720K CpG Island plus RefSeq promoter DNA methylation arrays which uses a competitive hybridization of methylated DNA immunoprecipitation (MeDIP) to input DNA. I understand that MeDIP-chip arrays can be analyzed using the CHARM analysis method with the charm R package in Bioconductor, but I am unsure of which parts of the R program need to be modified.
I was wondering if anyone has experience modifying the charm R program for MeDIP-chip arrays. My thought is that there are two parts that need to be changed: first, the definition of log2 ratio M needs to be changed to log2(635/532) where 635 is the MeDIP signal, and second, the part of the methp equation which defines the observed enriched signal intensity from "1-pi" to "pi".
Any insight would be greatly appreciated.