Processing ChIP-Chip Data: From the Scanner to the Browser

High-density tiling microarrays are increasingly used in combination with chromatin immunoprecipitation (ChIP) assays to delineate the regulation of gene expression. Besides the technical challenges inherent to such complex biological assays, a critical, often daunting issue is the correct interpretation of the sheer amount of raw data generated by utilizing computational methods. Here, we go through the main steps of this intricate process, including optimized chromatin immunoprecipitation on chip (ChIP-chip) data normalization, peak detection, as well as quality control reports. We also describe convenient standalone software suites, including our own, CoCAS, which works on the latest generation of Agilent high-density arrays, allows dye-swap, replicate correlation, and easy connection with genome browsers for results interpretation, or with, e.g., other peak detection algorithms. Overall, the guidelines described herein provide an effective introduction to ChIP-chip technology and analysis.