Dear all, We have performed a time-scale experiment including different time- points (0h, 2h, 6h, .). Treated and untreated cells were compared by competitive hybridizations on every time-point using dual-channel microarrays. Now we want to detect groups of genes affected by the same TFs using a gene clustering approach based on the set of differentially expressed genes. Is it generally appropriate to perform gene expression standardization (e.g. by rescaling and recentering) on logged fold changes using such an experimental design independently of the distance function used (e.g. euclidean distance, pearson correlation, cosine correlation, .)? What is the impact of such a standardization approach on the clustering results? I would appreciate any comments or suggestions. Regards, Serge Eifes Serge Eifes Laboratoire de Biologie Moleculaire et Cellulaire du Cancer (LBMCC) Hopital Kirchberg 9,rue Edward steichen L-2540 LUXEMBOURG