Hi Crispin & others, I was comparing the plier implementation you've done with Affymetrix's technical note on plier (http://www.affymetrix.com/support/technical/technotes/plier_technote. pdf) and some of the options don't seem to match. In Affy's technical note, after the normalization option there is a background step, with the options 'PM-MM', 'PM-B', 'PM only', and 'MM as additional PM'. However, in BioC's justPlier(), after the 'normalize' argument there is a 'norm.type' argument with options 'separate', 'pmonly', 'mmonly' or 'together'. Looking at the code, I see 'norm.type' gets pushed to normalize.AffyBatch.quantiles(). I take it 'norm.type' is just additional functionality added to the normalization step? How are the background options implemented? There are 'usemm' and 'usemodel' arguments in justPlier(), but there's no information given about them, other than the defaults are usemm=TRUE and usemodel=FALSE. I did create my own wrapper around justPlier to add the variance stabilization at the end (below). Because Affy's presentation of plier highlights the background correction options, it would be better if justPlier() had a more intuitive interface to them, with a better explanation in the help page. Adding the variance stabilization option would also enhance the user-friendliness of justPlier. Thanks, Jenny JDplier <- function (object, var.stab=T, stab.val=16, ... ) { object <- justPlier(object, ...) if (var.stab) exprs(object) <- log2(2 ^ exprs(object) + stab.val) return(object) } 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