[BioC] 2x2 factorial with dye effect, limma design

[Thomas Degenkolbe]

Hi,

I'm trying to set up a contrast matrix for my microarray experiment and
I'm not sure whether I did it in the right way. The experiment has a
2x2 factorial (S or T; c or d) design and samples (Sc, Sd, Tc, Td) were
hybridized in a loop design. I want to include the dye effect in the
design and calculate the contrasts for d vs. c; dT-cT; dS-cS and the
interaction [(dT-cT)-(dS-cS)].

Following the example for a single factor exp. in the user guide with
dye effect I tried this:

> design <- modelMatrix(targets, ref="Sc")
Found unique target names:
 Sc Sd Tc Td 
> design <- cbind(Dye=1, design)
> design
         Dye Sd Tc Td
Slide03   1  1  0  0
Slide04   1  0  1 -1
Slide05   1 -1  1  0
Slide06   1  0  0  1
Slide09   1  0 -1  0
Slide10   1  1  0 -1
Slide19   1 -1  1  0
Slide20   1  1  0  0
Slide21   1  0 -1  1
Slide22   1  0  0 -1
Slide23   1 -1  0  0
Slide25   1  0 -1  1
Slide27   1 -1  0  0
Slide28   1  0 -1  1

> contrast.matrix <- cbind(
+   "d-c"=c(0,0.5,-0.5,0.5),
+   "dT-cT"=c(0,0,-1,1),
+   "dS-cS"=c(0,1,0,0),
+   "Interaction"=c(0,-1,-1,1))
> rownames(contrast.matrix)<-colnames(design)
> contrast.matrix
     d-c dT-cT dS-cS Interaction
Dye  0.0     0     0     0
Sd   0.5     0     1    -1
Tc  -0.5    -1     0    -1
Td   0.5     1     0     1


Is this correct?

Thanks in advance,
Thomas Degenkolbe