[BioC] Limma with common Reference Design

[michael watson (IAH-C)]

Hi

Sorry, it's been a while since I worked with a common reference design,
so I may be repeating myself.

I have some data, two conditions both compared to a common reference
(which is always Cy3).  So targets looks something like this:

Array	Cy3	Cy5
1	ref	T1
2	ref	T1
3	ref	T1
4	ref	T2
5	ref	T2
6	ref	T2

What I want to do is find those genes which are differentially expressed
between T1 and T2 (in either direction; instinctively I want to use a
two-sample t-test).  So I have a design matrix so:

	T1	T2
1	0	1
2	0	1
3	0	1
4	1	0
5	1	0
6	1	0

And a contrasts matrix so:
	T1	T2	T1-T2
T1	1	0	1
T2	0	1	-1

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.

Thanks for any help!

Mick