

Hi Naira
I
used the mouse promoter tiling array to study the long term effects of two
drugs on DNA methylation in mouse liver.  I adapted the
Affy chromatin IP assay protocol to prepare the samples and make them ready for
hybridization with tiling arrays.  I have 3 groups (control, treatment A,
and treatment B) with 4 different replicates in each group.  For each
sample, I performed an immunoprecipitation and input which makes the total
number of chips 24 (3 groups X 4 mice X 2) the 2 means immunoprecipitation and
input.  


I
analyzed the data with TAS and MAT to determine the
methylation sites in the 3 groups.  However, I am interested in the
differential methylation between the control and the drug-treated groups. 
So far, all what I am doing is visually comparing the bar files of the 3 groups
in IGB and trying to find differences in methylation but this is not a
practical way to check all the chromosomes and there is no statistics behind
it.  Is there any package in BioC that deals with this issue?


Joseph






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