Hi, there, I'm working on a time-course microarray analysis and got some problems. The design is very simple. All the other time point samples were compared to time 0 and the comparison between every two connected time points were also made. So here is what I did: > library(limma) > targets=readTargets() > spottypes=readSpotTypes() > RG=read.maimages(targets, source="genepix") > RG$genes$Status=controlStatus (spottypes, RG) >RG=backgroundCorrect(RG, method="normexp", offset=50) >MA=normalizeWithinArrays(RG, method="loess") >MA=normalizeBetweenArrays(MA, method="quantile") >MA2=MA[MA$genes$Status=="cDNA",] >MAave = avereps (MA2, ID=MA2$genes$Name) ##### Then I separate the color channels so that I can make comparison between any two time points########### > targets2=targetsA2C(targets) > targets2 channel.col SlideNumber FileName Date Target 1.1 1 1 12h-R.gpr 3/19/2009 12hr 1.2 2 1 12h-R.gpr 3/19/2009 ref 2.1 1 2 R-12h.gpr 3/19/2009 ref 2.2 2 2 R-12h.gpr 3/19/2009 12hr 3.1 1 3 1D-R.gpr 3/24/2009 day1 3.2 2 3 1D-R.gpr 3/24/2009 ref 4.1 1 4 R-1D.gpr 3/24/2009 ref 4.2 2 4 R-1D.gpr 3/24/2009 day1 5.1 1 5 2D-R.gpr 3/24/2009 day2 5.2 2 5 2D-R.gpr 3/24/2009 ref 6.1 1 6 R-2D.gpr 3/24/2009 ref 6.2 2 6 R-2D.gpr 3/24/2009 day2 7.1 1 7 3D-R.gpr 3/26/2009 day3 7.2 2 7 3D-R.gpr 3/26/2009 ref 8.1 1 8 R-3D.gpr 3/26/2009 ref 8.2 2 8 R-3D.gpr 3/26/2009 day3 9.1 1 9 4D-R.gpr 3/26/2009 day4 9.2 2 9 4D-R.gpr 3/26/2009 ref 10.1 1 10 R-4D.gpr 3/26/2009 ref 10.2 2 10 R-4D.gpr 3/26/2009 day4 11.1 1 11 7D-R.gpr 3/31/2009 day7 11.2 2 11 7D-R.gpr 3/31/2009 ref 12.1 1 12 R-7D.gpr 3/31/2009 ref 12.2 2 12 R-7D.gpr 3/31/2009 day7 13.1 1 13 21D-R.gpr 3/31/2009 day21 13.2 2 13 21D-R.gpr 3/31/2009 ref 14.1 1 14 R-21D.gpr 3/31/2009 ref 14.2 2 14 R-21D.gpr 3/31/2009 day21 15.1 1 15 12h-1D.gpr 4/2/2009 12hr 15.2 2 15 12h-1D.gpr 4/2/2009 day1 16.1 1 16 1D-12h.gpr 4/2/2009 day1 16.2 2 16 1D-12h.gpr 4/2/2009 12hr 17.1 1 17 1D-2D.gpr 4/2/2009 day1 17.2 2 17 1D-2D.gpr 4/2/2009 day2 18.1 1 18 2D-1D.gpr 4/2/2009 day2 18.2 2 18 2D-1D.gpr 4/2/2009 day1 19.1 1 19 2D-3D.gpr 4/14/2009 day2 19.2 2 19 2D-3D.gpr 4/14/2009 day3 20.1 1 20 3D-2D.gpr 4/14/2009 day3 20.2 2 20 3D-2D.gpr 4/14/2009 day2 21.1 1 21 3D-4D.gpr 4/14/2009 day3 21.2 2 21 3D-4D.gpr 4/14/2009 day4 22.1 1 22 4D-3D.gpr 4/14/2009 day4 22.2 2 22 4D-3D.gpr 4/14/2009 day3 23.1 1 23 4D-7D.gpr 4/16/2009 day4 23.2 2 23 4D-7D.gpr 4/16/2009 day7 24.1 1 24 7D-4D.gpr 4/16/2009 day7 24.2 2 24 7D-4D.gpr 4/16/2009 day4 25.1 1 25 7D-21D.gpr 4/16/2009 day7 25.2 2 25 7D-21D.gpr 4/16/2009 day21 26.1 1 26 21D-7D.gpr 4/16/2009 day21 26.2 2 26 21D-7D.gpr 4/16/2009 day7 > u=unique(targets2$Target) > lev=c("12hr","ref","day1","day2","day3","day4","day7","day21") > f=factor(targets2$Target, levels=lev) > design=model.matrix(~0+f) > design f12hr fref fday1 fday2 fday3 fday4 fday7 fday21 1 1 0 0 0 0 0 0 0 2 0 1 0 0 0 0 0 0 3 0 1 0 0 0 0 0 0 4 1 0 0 0 0 0 0 0 5 0 0 1 0 0 0 0 0 6 0 1 0 0 0 0 0 0 7 0 1 0 0 0 0 0 0 8 0 0 1 0 0 0 0 0 9 0 0 0 1 0 0 0 0 10 0 1 0 0 0 0 0 0 11 0 1 0 0 0 0 0 0 12 0 0 0 1 0 0 0 0 13 0 0 0 0 1 0 0 0 14 0 1 0 0 0 0 0 0 15 0 1 0 0 0 0 0 0 16 0 0 0 0 1 0 0 0 17 0 0 0 0 0 1 0 0 18 0 1 0 0 0 0 0 0 19 0 1 0 0 0 0 0 0 20 0 0 0 0 0 1 0 0 21 0 0 0 0 0 0 1 0 22 0 1 0 0 0 0 0 0 23 0 1 0 0 0 0 0 0 24 0 0 0 0 0 0 1 0 25 0 0 0 0 0 0 0 1 26 0 1 0 0 0 0 0 0 27 0 1 0 0 0 0 0 0 28 0 0 0 0 0 0 0 1 29 1 0 0 0 0 0 0 0 30 0 0 1 0 0 0 0 0 31 0 0 1 0 0 0 0 0 32 1 0 0 0 0 0 0 0 33 0 0 1 0 0 0 0 0 34 0 0 0 1 0 0 0 0 35 0 0 0 1 0 0 0 0 36 0 0 1 0 0 0 0 0 37 0 0 0 1 0 0 0 0 38 0 0 0 0 1 0 0 0 39 0 0 0 0 1 0 0 0 40 0 0 0 1 0 0 0 0 41 0 0 0 0 1 0 0 0 42 0 0 0 0 0 1 0 0 43 0 0 0 0 0 1 0 0 44 0 0 0 0 1 0 0 0 45 0 0 0 0 0 1 0 0 46 0 0 0 0 0 0 1 0 47 0 0 0 0 0 0 1 0 48 0 0 0 0 0 1 0 0 49 0 0 0 0 0 0 1 0 50 0 0 0 0 0 0 0 1 51 0 0 0 0 0 0 0 1 52 0 0 0 0 0 0 1 0 > colnames(design)=lev > fit=lmFit(MAave, design) Error in lm.fit(design, t(M)) : incompatible dimensions Does anyone know what is wrong with this? Thanks. Wei -- Wei Xu Aquatic Animal Health Laboratory Pathobiology and Diagnostic Investigation College of Veterinary Medicine Michigan State University East Lansing, MI, 48824 Tel: 1-517-432-8258 [[alternative HTML version deleted]]