[BioC] Limma and creating design matrices for complex loop designs

[michael watson (IAH-C)]

Hi

I would like to respectfully request more examples of the creation of
design matrices for complex (ie involving more than 3 samples) loop
designs using two-colour microarrays in the limma documentation.

Although section 20.5 does give an example, with 5 RNA samples, one of
these is a pool which makes an obvious reference when creating the
design matrix as it is a coefficent we are not interested in estimating.
However, other loop designs may not contain such an obvious sample, and
I am struggling to figure out a way to create a design matrix for my
current design that allows all contrasts of interest.  In fact, at
present, I have to create one design matrix to get some of the contrasts
and another to get the rest.  Is this a valid approach?

Many thanks

Mick