[BioC] "charm" for MeDIP?

Johnny ql16717 at gmail.com
Mon Mar 5 22:33:30 CET 2012

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

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?


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