Identify Differentially Methylated Regions From Medip-Tiling-Array Data

Question

[Allpowerde]

Has anyone had experience with MeDIP-type protocols and nimbelgen "Mouse DNA Methylation 3x720K CpG Island Plus RefSeq Promoter" array with the cy3 (green) channel containing input, and the cy5 (red) channel containing methyl-enriched DNA?

I would like to identify the differentially methylated areas, which means I need to a) normalize the probes within and between arrays b) identify what is a methylated area c) quantify the difference between two such areas across multiple conditions

I would like to use CHARM but ran into some issues and was wondering if someone has experience with these analyses and can advise what tools to use.

Answer 1

[brentp]

What problems are you running into with CHARM? I use it for our analyses. The only problems I've seen are that it uses a lot of memory.

Often, we just use the R CHARM package to extract the normalized methp score (background-corrected, normalized within and between samples, genome-smoothed, and scaled) and use that for down-stream analyses.

The CHARM package allows you to find DMR's doing essentially a T-Test, but we use fit more complicated models on the extracted methp data that include covariates for age, gender, etc.

One other option is that nimblegen has just released some new software to find DMR's, you'll have to sign an MTA, but from the presentation I saw, it looked to be an improvement of the R CHARM package.

Again, if you give more info on the issues you are seeing, I can add more detail. (or at least commiserate)