[BioC] Analyzing MeDIP-Chip data - using Affymetrix promoter array

[Adrian Johnson]

Dear Group,
I am interested in identifying methylation changes in cell line after
treating with estradiol.

I have MCF10A cell line. I treated with two different concentrations
of estradiol (concA, and concB). I want to identify methylation
changes between no treatment and treatment and between two different
concentrations.


Controls:
MCF10A + 5mC -> ChIP -> Chip
MCF10A + IgG -> ChIP -> Chip

Treatment
MCF10A + 5 units of Estradiol  -----> MeDIP -> Chip
MCF10A + 8 units of Estradiol ------> MeDIP -> Chip


First I want to be able to identify if 5mC is specific to methyl
regions by comparing CEL file to IgG cel file.
then I want to compare treatment vs control and later treatment vs treatment.

I have been using MAT, but dont know how to make two controls in one
tag file.  Also I am not seeing much peaks.

I would like to know if there are any methods in bioconductor that
will help identify enriched peaks.

Thank you.

Ad.