Hello all, It appears that normalizeWithinArrays by default takes the weights in an RGList into account when doing a normalization, but this does not appear to be an option for normalizeBetweenArrays. I am correct that currently normalizeBetweenArrays will use all the values equally for whichever norm method is chosen? If so, could this option be added in the future? I think I can hack the scale part of the code for my own purposes now... Thanks, Jenny Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu