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

[Gordon Smyth]

At 09:20 PM 12/12/2005, michael watson \(IAH-C\) wrote:
>I think perhaps I was just getting confused.
>
>The function modelMatrix() throws an error message unless the number of
>columns you want in the design matrix is one less than the number of RNA
>targets.  This led me to get confused as to how you could create all
>contrasts of interest if one was missing from the design matrix.
>
>However, if we have four RNA targets (R1-4) in a loop design, we can
>choose arbitrarily to use one as the ref:
>
>modelMatrix(Targets, ref="R1")
>
>Then apply our contrasts of interest R2-R3, R3-R4, R2-R4 and then any
>comparisons to R1 are simply R2, R3 and R4.... Correct?

Exactly.

Gordon

>Mick