Dear list, I would like to apply the Rank Products method in a two-color experiment on breast cancer data in order to identify differentially expressed genes between ER+ and ER- samples. I downloaded the R-package RankProd and tried to use the RP function. The experiments were done with a common reference for all the samples examined. So the sample of interest was at the one channel and the reference on the other. I was wondering in the RP function: RP(data,cl,num.perm=100,logged=TRUE,na.rm=FALSE,gene.names=NULL,plot=F ALSE, rand=NULL), where cl is said to be: cl: a vector containing the class labels of the samples. In the two class unpaired case, the label of a sample is either 0 (e.g., control group) or 1 (e.g., case group). For one class data, the label for each sample should be 1. Can I use 1 for ER- and 0 for ER+ samples from the matrix that I have? My matrix contains gene expressions as rows and samples as columns. The columns are only the samples of interest (ER+, ER-), not the reference. I am a bit confused with the exact meaning of "control group" and "case group". Thanks a lot! Eleni [[alternative HTML version deleted]]