[BioC] confusion using model.matrix with two-color arrays in limma
Dick Beyer
dbeyer at u.washington.edu
Mon Nov 1 22:55:12 CET 2004
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
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