Hi, I'm trying to use duplicateCorrelation for duplicate spots with no success. My array design includes three replicas of each spot, 120 spots apart so I use: cor <- duplicateCorrelation(MA,design,ndups=3,spacing=120) correlation <- cor$consensus.correlation fit <- lmFit(MA,design,ndups=3,spacing=120,correlation=correlation) That works when I analyze a simple experiment with a design of (1,-1). But when I have the following design: ad em l1 l2 l3 l4 V3_slide11 0 -1 0 0 0 0 V3_slide14 0 0 -1 0 0 0 V3_slide15 0 0 0 -1 0 0 V3_slide16 0 0 0 0 -1 0 V3_slide17 0 0 0 0 0 -1 V3_slide18 -1 0 0 0 0 0 I can not get the correlation so I have to use the default 0.75 correlation for lmFit in order to work. Thanks in advance, Sergio