If I have a matrix of only a single class, why do the results seem to have two sets of values for two different classes ? > ncol(aMatrix) [1] 3 > RPanalysis <- RP(data = aMatrix, cl = rep(1, 3), num.perm = 1000) > head(RPanalysis[[1]]) class1 < class2 class1 > class 2 1 0.8730351 0.9438351 2 0.8708771 0.9556519 3 0.8579349 0.9439297 4 0.9870283 1.2435040 5 0.8855495 1.1302624 6 0.8874949 0.9434583 Even the progress message says "Rank Product analysis for one-class case". The vignette gives an example of creating an RP object for a single class, so I'm sure that the program should work correctly for ranking genes in a single class. -------------------------------------- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia