Hi, I have some Agilent RNA data for which there are only 2 conditions and single color and each condition is applied to separate chips. Without scaling I got a 10,000 of differentially expressed genes with less than 8% FDR. After scaling the number of differential genes decreased to ~6,000 with less than 16% FDR. The chips obviously need to be scaled. Does anyone have any recommendations for normalization? Lana Schaffer Biostatistics/Informatics The Scripps Research Institute DNA Array Core Facility La Jolla, CA 92037 (858) 784-2263 (858) 784-2994 schaffer at scripps.edu