Dear Prof. Gorden: Thank you very much for your help. I am sorry for not telling the enough information. I have two two-colour arrays to analyze. Each probe is present three times on each chip side by side. I use Genepix to get the gps files. Here is my session information and functions. > sessionInfo() R version 2.2.0, 2005-10-06, i386-pc-mingw32 attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" >library(limma) >targets >myfun<-function(x,threshold=50){ okred<-abs(x[,"F635 Median"]-x[,"F635 Mean"])<threshold okgreen<-abs(x[,"f532="" median"]-x[,"f532="" mean"])<threshold="" as.numeric(okgreen="" &="" okred)="" }="">RG <- read.maimages(targets$Filename, source="genepix", wt.fun=myfun) >RG$printer <- getLayout(RG$genes) >RG <- backgroundCorrect(RG, method="normexp", offset=50) >MA<-normalizeWithinArrays(RG,layout,method="loess") >design<-c(1,1) >library(statmod) >cor <- duplicateCorrelation(MA,design,ndups=3) >cor$consensus.correlation >fit<-lmFit(MA,design,ndups=3,correlation=cor$consensus.correlation) The consensus correlation returned by duplicateCorrelation is -0.5. And when I input "fit<-lmFit(MA,design,ndups=3,correlation=cor$consensus.correlation)" ,it complains an error on chol(V). Questions: (1) why this error comes out? (2) If the cor$consensus.correlation value is negative, could I use the function "fit<-lmFit()"? If not, what is the range of the cor$consensus.correlation that I can use in the function "fit<-lmFit()". (3) Do I or must I need swap the dyes for my experiment? (4) Do I need use function "MA <- normalizeBetweenArrays(MA)" when I use the function "fit<-lmFit()"?