Why do I get an error message when running ComBat? Target file: SAMPLE DAYPREP HOMA x5794 1 IS x5803 1 IS x5810 1 IR x5811 1 IR x5828 1 IS x5829 1 IS x5834 2 IR x5849 2 IR x5857 2 IS x5859 2 IS x5861 2 IS library (limma) library(Biobase) library(statmod) library(sva) eset.txt<-read.delim("eset.txt",header=TRUE) target<-read.delim("target.txt",header=TRUE) eset<-readExpressionSet("eset.txt","target.txt",header=TRUE) HOMA <- factor(target$HOMA, levels=c("IS","IR")) batch <- target$DAYPREP design <- model.matrix(~as.factor(HOMA), data=target) combateset <- ComBat(dat=eset, batch=batch, mod=design) -- output of sessionInfo(): Found 2 batches Found 1 categorical covariate(s) Standardizing Data across genes Error in dat - t(design %*% B.hat) : non-numeric argument to binary operator In addition: Warning message: In is.na(dat) : is.na() applied to non-(list or vector) of type 'S4' -- Sent via the guest posting facility at bioconductor.org.