[BioC] Limma with common Reference Design

[Sean Davis]

On Oct 8, 2004, at 10:57 AM, michael watson (IAH-C) wrote:

>
> Is this right?  From reading the examples, I think it is, but I am not
> sure what the advantage is of having the contrasts matrix as well as 
> the
> design matrix, adding the contrasts matrix certainly gives me different
> results to just using the design matrix alone.  Hmmmmm.
>

Mick,

The answer depends on what you want to get?  I am assuming that you 
actually want to have T1-T2, so you do need the contrast matrix.  You 
don't get that quantity directly from the design matrix, so there is no 
comparable answer using a design matrix alone as compared to including 
a contrast matrix.  The first two coefficients for each should be the 
same, though.

Sean