Hi, It is possible that my only problem is that I'm trying to use duplicateCorrelation with few arrays but I just wanted to be sure. My slides include three replicas of each spot 120 spots apart; to make sure I'm giving duplicateCorrelation the right input I do: unwrapdups(MA$genes$Name, ndups=3, spacing=120) and I do obtain a matrix with identical columns with the replica spots on it. My problem is that when I try to calculate: cor <- duplicateCorrelation(MA,design,ndups=3,spacing=120) I get several warnings: 1: NaNs produced in: sqrt(dfitted.values) and I get a correlation of 1. Right now I do not have two more arrays than the column rank of design, but I was still trying to get some results; is this the problem or is there something I'm doing wrong. Thanks in advance for your help, Sergio