Abstract:To perform a quantitative analysis with gene-arrays, one must take into account inaccuracies (experimental variations, biological variations and other measurement errors) which are seldom known. In this paper we investigated amplifi cation and noise propagation related errors by measuring intensity dependent variations. Based on a set of control samples, we create confi dence intervals for up and down regulations. We validated our method through a qPCR experiment and compared it to standard analysis methods (including loess normalization and fi ltering methods based on genetic variability). The results reveal that amplifi cation related errors are a major concern.