[BioC] "charm" for MeDIP?

[Johnny]

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