Hi there!

It's a common concern when we are designing our matrix with edgeR. Note I have the follow colData:

condition                time                group
mock                      4                  mock.4
mock                      12                 mock.12
treated                   4                  treated.4
treated                   12                 treated.12

My purpose is to make contrasts among different groups, using a design matrix as:

group <- colData$group
design <- model.matrix(~ group)
colnames(design) <- levels(group)
design

However, when I use this matrix, including ~0

group <- colData$group
design <- model.matrix(~ 0 + group)
colnames(design) <- levels(group)
design

I get different results, why? what is the difference? and what is suitable?

Thanks in advance!