All, I'm using R v2.0.1, affy v1.5.8 and Biobase v1.5.0. I'm using Affy data for classification. I have a training data set which I use to process the data (rma, center, scale etc.) for use with various models. Once I get the models trained, I'll be applying them to future data as they come in. During the data processing, I can save the information about the training set - for example, the means and variances for each probe. I can use these to center and scale new samples without problems. I'm not quite sure to do about the rma step though. The quantile normalization was not hard to adapt based on modifying limma's normalizeQuantiles function. In that case, I can just feed in a pre-normalized sample, get its quantiles and normalize the new samples to this reference distribution. The other steps in rma do not appear to be so simple, such as the median polish. Has anyone implemented code to apply rma on new samples based on previous data? If not, any suggestions on the approach? Thanks in advance, Max LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}