ChIP-chip (or ChIP-on-chip) is a technology for isolation and identification of genomic sites occupied by specific DNA binding proteins in living cells. The ChIP-chip data can be obtained over the whole genome by tiling arrays, where a peak in the signal is generally observed at a protein binding site. In this paper, we describe and present a probability theory for modelling ChIP-chip data. We then propose a model-based computational method for locating and testing peaks for the purpose of identifying potential protein binding sites.
