[BioC] Advice for ChIPchip-Analysis

[Karin Zimmermann]

Hello all,

I have ChIP-chip and expression data for six different cell-lines. I am 
new to ChIP-Chip analysis and would therefore need some advise to 
analyse them correctly.

Our experimental setting is:
For each of the six celllines, three immuno-precipitated and three non 
specific (IgG) chips (Affymetrix Promoter Tiling Array 1.0R) have been 
spotted, resulting in 36 chips. The six celllines are divided in two 
groups, for the sake of convenience I call them group A and B. Our 
research group is interested in differences between the two groups. So 
in patterns which differentiate the two groups. To be precise, we are 
interested in genes which are significantly enriched in group A but not 
B and vice versa.

What would be a good approach to perform such kind of analysis? The 
publications concerning chIP-chip analysis (like MAT, Ringo, and others) 
I've read sofar describe the data analysis to find chIP enriched region. 
But I'm interested in regions/genes which are differentially enriched 
between group A and group B.

Thanks in advance.
Karin 
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