Hi again! I thought it might be better to add some information to my message concerning my problem using the duplicateCorrelation function in Limma (see below). The arrays are used are printed in duplicates with a spacing of 15000 (so in total 30000 features per array) and I did the imageprocessing using GenePixPro6.1. This is what I have done before applying the dupcor-function: > targets=readTargets("Targets_basicSat.txt") > targets SlideNumber FileName Cy3 Cy5 1 1 3096_basicSat.gpr ref A 2 2 3079_basicSat.gpr A ref 3 3 3089_basicSat.gpr ref A 4 4 3081_basicSat.gpr A ref 5 5 3071_basicSat.gpr ref B 6 6 3082_basicSat.gpr B ref 7 7 3085_basicSat.gpr ref B 8 8 8268_basicSat.gpr B ref 9 9 7829_basicSat.gpr ref C 10 10 3086_basicSat.gpr C ref 11 11 7823_basicSat.gpr ref C 12 12 7826_basicSat.gpr C ref 13 13 3090_basicSat.gpr ref D 14 14 3091_basicSat.gpr D ref 15 15 3092_basicSat.gpr ref D 16 16 7827_basicSat.gpr D ref Every other slide is a dyeswapped technical replicate and per "group" (A,B,C,D) there are 2 biological replicates. > K=read.maimages(targets$FileName, source="genepix.median", wt.fun=wtflags(0)) > types=readSpotTypes("SpottypesGAPDH.txt") > Status=controlStatus(types, K) > K$genes$Status=Status > K2=backgroundCorrect(K, method=?subtract?) > K2=normalizeWithinArrays(K2, method="median") > design=modelMatrix(targets, ref="ref") > design A B C D [1,] 1 0 0 0 [2,] -1 0 0 0 [3,] 1 0 0 0 [4,] -1 0 0 0 [5,] 0 1 0 0 [6,] 0 -1 0 0 [7,] 0 1 0 0 [8,] 0 -1 0 0 [9,] 0 0 1 0 [10,] 0 0 -1 0 [11,] 0 0 1 0 [12,] 0 0 -1 0 [13,] 0 0 0 1 [14,] 0 0 0 -1 [15,] 0 0 0 1 [16,] 0 0 0 -1 >cor=duplicateCorrelation(K2, design=design, ndups=2, spacing=15000, weights=K2$weights) And at this point, I get the warning message "NaNs produced in: sqrt(dfitted.values)" and I do not know if I should simply procede or if this warning indicates a major problem. I hope somebody can help and that this is sufficient information. Kind regards, Dorthe Hi, when using the dulicateCorrelation function I get the following warning message: "NaNs produced in: sqrt(dfitted.values)" I have used the function before and usually got the "too much damping" warning message, which I know can be ignored. But now I get the warning message metioned above and don't know whether to ignore it or not. Thanks for any help in advance, Dorthe -- Dorthe Belgardt Institute of Basic Medical Sciences Department of Physiology P.O. Box 1103 Blindern 0317 Oslo Norway -- Dorthe Belgardt Institute of Basic Medical Sciences Department of Physiology P.O. Box 1103 Blindern 0317 Oslo Norway Tel: 0047-22851295