F Duan wrote: > Default should be "quantile" if I remember correct. That's right. To be precise, it is the default in: getOption("BioC")$affy$normalize.method (this was done for a future-but-yet-to-come scheme to let one specify default methods in a R config file ... possibly the setHook methods can let one do so, no time to investigate it... there is also few lines about the package options in the affy vignette about cdfenvs). > Quoting gregory voisin <voisingreg@yahoo.fr>: >>which difference betwen >>datanormal<-normalize(data) >>datanrormal<-rma(data) 'normalize' just performs the 'normalization' step (or whatever name you may want to give it) at the probe level. 'rma' does the full monty: from raw probe level data to probe sets expression values. This is mainly a handy wrapper for the function 'expresso' with the set of pre-processing methods proposed by the rma authors. hth, Laurent