I have two color (Agilent) ChIP-chip data on two different cell types (lets say IP1 and IP2 for cell type1 and cell type2 respectively). I want to get differential binding locations (probes) with Log ratio.
For example: What I want is to compare:
(IP1/input1 versus IP2/input2)
Q: How can I do that ? Q: Is there any tools/software/package that does this job? There are some tools for such analysis with ChIP-seq data, but I am looking something for two color ChIP-chip data.