Hi all Sorry I've asked on this topic before but I'm still confused. This time... 6 Imagene arrays. Targets file : "Name " "FileNameCy3" "FileNameCy5" "Cy3" "Cy5" "5636-T56-Br.1-3.txt" "5636-P119-Br.1-5.txt" "T56" "P119" "2280-P119-Br.1-3.txt" "2280-T56-Br.1-5.txt" "p119" "T56" "9187-T56-Br.2-3.txt" "9187-P119-Br.2-5.txT" "T56" "P119" "7157-P119-Br.2-3.txt" "7157-T56-Br.2-5.txt" "p119" "T56" "9189-T56-Br.4-3.txt" "9189-P119-Br.2-5.txt" "T56" "P119" 2282-P119-Br.1-3.txt" "2282-T56-Br.3-5.txt" "p119" "T56" 1&2 and 3&4 are technical replicates (dye-swaps), 5&6, though dye swaps, are also different biological samples . so is this correct? design <- c(1, -1, 1, -1, 1, -1) biolrep <- c(1, 1, 2, 2, 3, 4) and can I use duplicatedCorrelation?... corfit <- duplicateCorrelation(MA, design, ndups = 1, block = biolrep) fit <- lmFit(MA, design, block = biolrep, cor = corfit$consensus) (I get over 50 warnings when I do use duplicateCorrelation) Thanks Glyn This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.