 This raw data, encoded as false-color image, needs to be converted to numerical values before the actual analysis can be done.The analysis and information extraction of the raw data often remains the most challenging part for ChIP-on-chip experiments.Problems arise throughout this portion of the workflow, ranging from the initial chip read-out, to suitable methods to subtract background noise, and finally to appropriate algorithms that normalize the data and make it available for subsequent statistical analysis, which then hopefully lead to a better understanding of the biological question that the experiment seeks to address.