ChIP-Chip microarray data analysis is a multi-step approach that requires several different applications to progress from the initial stages of raw data analysis to the identification and characterization of ChIP-binding sites. There are multiple approaches to data analysis and several applications available for each stage of the analysis pipeline. Each application must be evaluated for its suitability for the particular experiment as well as the researcher’s computer background. This chapter is a review of the commonly available applications for Affymetrix ChIP-Chip data analysis, as well as the general workflow of a ChIP-Chip analysis approach. The purpose of the chapter is to allow the researcher to better select the appropriate applications and provide them with the direction necessary to proceed with a ChIP-Chip analysis.
