Are there any statistical tests that are applied to my ChIP-chip data?
Yes, we determine the false discovery rate (FDR) for each peak identified from the scaled log2-ratio data. First the scaled log2-ratio data is analyzed to identify peaks above a specified cutoff value. Assume we find 20 peaks that are above this cutoff value; the scaled log2-ratio data is then randomized 20 different times and after each permutation it is determined how many peaks are still above the cutoff value. So, if after randomizing the data 20 times we find that there are 2 peaks above the cutoff value, the FDR is 10% (which is a reasonably good FDR value). FDR values can differ depending on the peak height and number of probes comprising the peak. On SignalMap, the peaks will be color coded corresponding to FDR value for quick identification of statistically significant peaks.
