Chromatin immunoprecipitation (ChIP) combined with DNA microarray is a high-throughput technology to investigate DNA-protein binding or chromatin/histone modifications. ChIP-chip data require adapted statistical method in order to identify enriched regions. All methods already proposed are based on the analysis of the log ratio (Ip/Input). Nevertheless, the assumption that the log ratio is a pertinent quantity to assess the probe status is not always veri.ed and it leads to a poor data interpretation.