[BioC] contrasts in limma and missing values

[Hans-Ulrich Klein]

Dear List,

I have a question concerning missing values in limma. Consider the 
following short example:

M = rbind(c(10,9,5,4,5,12,13,7,8),c(10,9,5,4,5,12,13,7,8))
w = rbind(c(1,1,1,1,1,1,1,1,1),c(1,1,1,1,1,0,0,0,0))
class = factor(c(1,1,2,2,2,1,1,2,2))
lab = factor(c(1,1,1,1,1,2,2,2,2))

design =  model.matrix(~ 0 + class + lab)
contrasts = makeContrasts(contrasts="class1-class2", levels=design)

fit = lmFit(M, design=design, weights=w)
fit2 = contrasts.fit(fit, contrasts)

Obviously, the effect of "lab" can not be estimated for gene 2. All 
measurements of gene 2 in lab2 have weights = 0. However, the contrast 
of interest (here class1 - class2) can be estimated by using the 
observations from lab1, but in the limma-object (fit2 in the example 
above) the contrast is NA. Can someone explain me whether/why this is 
sensible?

Thanks for your help,
Hans-Ulrich