[BioC] how to make makeContrast in edgeR?

[wang peter]

it also generate another problem

if i use one factor, as you suggested :  control_0h, control_0h, ...,
treated_0h, ..., treated_48h, etc.

design = model.matrix( ~ fac)
contmat = makeContrasts(treated_6h-control_6h,treated_12h-control_12h)

will the glm use all the samples to do regression for single comparision?

i hope glm use all to do regression, even on single test
like:treated_6h-control_6h