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

[Gordon Smyth]

>Date: Fri, 9 Dec 2005 11:21:49 -0000
>From: "michael watson \(IAH-C\)" <michael.watson at bbsrc.ac.uk>
>Subject: [BioC] Limma and creating design matrices for complex loop
>         designs
>To: <bioconductor at stat.math.ethz.ch>
>
>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?

Valid if both design matrices span the full treatment space, but never 
necessary.

Gordon

>Many thanks
>
>Mick