Hello, I have Illumina 450k methylation data sets for 20 males (10 cases and 10 controls) and 20 females (10 cases and 10 controls), which I have been analyzing separately using MINFI and LIMMA. The phenotype that defines the cases and controls is the same for both data sets. Is there any way to combine both data sets into one and analyze differential methylation using sex as a covariate (with LIMMA)? Here is the script that I am using: dat <- read.450k.exp(base=basedir) targets <- read.table("target.txt", sep="\t", header=T, as.is=T) swan <- preprocessSWAN(dat2) M <- getM(swan) des <- model.matrix(~-1+targets2$Status) colnames(des) <- c("CASE","CONTROL") cont <- makeContrasts(CASE-CONTROL, levels=des) fit <- lmFit(M, des) fit2 <- eBayes(contrasts.fit(fit, cont)) vennDiagram(decideTests(fit2, p.value=0.001, adjust.method="BH")) Thanks a lot in advance! Best regards, Jukka MSc [[alternative HTML version deleted]]