[BioC] confusion using model.matrix with two-color arrays in limma

[Dick Beyer]

I am struggling with trying to use model.matrix, which is straight-forward for 
single color arrays, on two-color dye-swap data. For two-color data, using modelMatrix is simple and straight-forward.

I would like to know how to sort of combine these two calls, model.matrix and modelMatrix, so I can easily specify my design matrix (with modelMatrix), and easily specify complex contrasts (as with model.matrix).

My particular experiment is a 2x2x2 design with factors, T,R,C each having levels 0/1.  I would like to specify the interaction T*R*C, without having to explicitly type it out using makeContrasts().

How can I use model.matrix() so the dye-swaps are combined correctly (as is done easily with modelMatrix), or how can I specify makeContrasts() so I don't have to type out the T*R*C interaction?

My targets are (where H signifies the case for parameter T=0, T signifies parameter T=1, etc):
 	Cy3	Cy5
1	REF	HC
2	HC	REF
3	REF	HRC
4	HRC	REF
5	REF	TC
6	TC	REF
7	REF	TRC
8	TRC	REF
9	REF	T
10	T	REF
11	REF	TR
12	TR	REF
13	REF	H
14	H	REF
15	REF	HR
16	HR	REF
My parameters are:
 	T	R	C
1	0	0	1
2	0	0	1
3	0	1	1
4	0	1	1
5	1	0	1
6	1	0	1
7	1	1	1
8	1	1	1
9	1	0	0
10	1	0	0
11	1	1	0
12	1	1	0
13	0	0	0
14	0	0	0
15	0	1	0
16	0	1	0

If I use the modelMatrix and makeContrast approach, I would use something like the following to get the T*R*C interaction: 
design <- modelMatrix(targets,ref="REF")
fit <- lmFit(RG, design)
contrast.matrix <- makeContrasts("H-HC-HR+HRC-T+TC+TR-TRC",levels=design)
fit2 <- contrasts.fit(fit, contrasts.matrix)

If I use the model.matrix approach (ignoring the necessary dye-swapping):
dd <- data.frame(
T=factor(c(0,0,0,0,1,1,1,1,1,1,1,1,0,0,0,0)),
R=factor(c(0,0,1,1,0,0,1,1,0,0,1,1,0,0,1,1)),
C=factor(c(1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0)))
design.lm <- model.matrix(~  T*R*C, data=dd, contrasts = list(T="contr.sum", R="contr.sum", C="contr.sum"))
fit <- lmFit(RG, design.lm)
and have no need for the contrasts.fit() call.

If I knew how to correctly specify a dye-flip parameter in the "dd" data.frame, I think I would be where I'd like to be.

Any help or suggestions to try from anyone would be greatly appreciated.
Thanks very much,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html