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

Adrian Johnson oriolebaltimore at gmail.com
Fri Mar 20 19:18:37 CET 2009

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

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

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.


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