Dear List, I am using limma to analyze a affy ST1.0 dataset. I have 6 patients from which I have two tissue types: tumor and non- tumor. One of the sample has a technical repeat, resulting 12 arrays. I would like to compare tumor vs. non-tumor and incorporate the pairing and technical repeats information into the analysis. However, I got error when I tried to calculate the correlation using duplicatedCorrelation function(please see code below). Therefore, I cannot do limma fit as usual. > library(limma) > target<-read.table("target.txt",header=T,sep="\t") > target FileName Type Tumor Patient Repeat 1 8671-596NT.CEL ADENO N 1 1 2 8672-543T.CEL ADENO Y 2 2 3 8674-558T.CEL ADENO Y 3 3 4 8675-558NT.CEL ADENO N 3 4 5 8676-560T.CEL ADENO Y 4 5 6 8677-560NT.CEL ADENO N 4 6 7 8679-596NT2.CEL ADENO N 1 1 8 8686-507T.CEL ADENO Y 5 7 9 8687-507NT.CEL ADENO N 5 8 10 8688-507NTb.CEL ADENO N 5 9 11 8689-538T.CEL ADENO Y 6 10 12 8690-538NT.CEL ADENO N 6 11 > F<-factor(target$Tumor,levels=c("N","Y")) > Patient<-factor(target$Patient) > design<-model.matrix(~Patient+F) > design (Intercept) Patient2 Patient3 Patient4 Patient5 Patient6 FY 1 1 0 0 0 0 0 0 2 1 1 0 0 0 0 1 3 1 0 1 0 0 0 1 4 1 0 1 0 0 0 0 5 1 0 0 1 0 0 1 6 1 0 0 1 0 0 0 7 1 0 0 0 0 0 0 8 1 0 0 0 1 0 1 9 1 0 0 0 1 0 0 10 1 0 0 0 1 0 0 11 1 0 0 0 0 1 1 12 1 0 0 0 0 1 0 > corfit<-duplicateCorrelation(intensity,design,ndups=1,block=target$R epeat) Loading required package: statmod > fit<-lmFit(intensity,design,block=target$Repeat,cor=corfit$consensus) Error in backsolve(cholV, t(M), transpose = TRUE) : NA/NaN/Inf in foreign function call (arg 1)fit<-eBayes(fit) Hope someone can help me to figure out the problem . Thanks! Juan Lin AECOM [[alternative HTML version deleted]]