ChIP-chip (Chromatin immunoprecipitation followed by microarray (chip) ananlysis, also known as “”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 dissertation, a probability
theory for modelling ChIP-chip data will be presented and a model-based computational method is proposed for locating and testing peaks for the purpose of identifying potential protein binding sites. Approaches to adjust p-values for multiple test settings are also proposed.