Hello, I have a question that may be so basic in class prediction that I can't even find any discussion on it anywhere: What effect does between- array normalization of microarray data, particularly those methods that normalize to a particular group of arrays, have on class prediction algorithms? Based on my scant knowledge of class prediction with microarray data and the few details I found in the literature, prediction algorithms are generated from a set of data that is variously divided into training and test tests, and possibly subdivided as well... but this entire set of data is likely to be normalized together. How should a future, independent set of arrays, or in particular, a single array, be handled in regards to normalization before the prediction algorithm is applied? Do others see that this is a potential problem, or am I imagining it? I hope this question is in the scope of the Bioconductor list, but if not, would someone please direct me to a person or place that could answer my question? Thank you, 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