hi,

when I using edgeR to identify differentially methylated regions (DMR) between different groups with edgeR guidepaper, I have a question about the design matrix .

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> sam <- rep(samples, each=2) > meth <- factor(rep(c("Me","Un"),6), levels=c("Un","Me")) > design <- model.matrix(~ sam + meth) > colnames(design) <- gsub("sam","",colnames(design)) > colnames(design) <- gsub("meth","",colnames(design)) > colnames(design)[1] <- "Int" > design <- cbind(design, + Me2=c(0,0,0,0,1,0,1,0,0,0,0,0), + Me3=c(0,0,0,0,0,0,0,0,1,0,1,0))

The 7th column “Me” represents the methy-lation level (or M-value) in the 40-45 µm group. The 8th column “Me2” represents the differencein methylation level between the 50-55 and the 40-45 µm groups. Finally, the last column “Me3”

represents the difference in methylation level between the 60-65 and the 40-45 µm groups.

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the contents above from edgeR guide, my question is how to to design the contrast column like 8th column.

intercept group is 40-45cm?

if i want to compare the 50-55cm group to 60-65cm group,how to do?I get a answer ,design matrix in GLM .is it ok for edgeR?

the method of edgeR or limma to identify differential analysis is that regressing each group with linear model,then contrast the different groups' regression to identify difference ?