[BioC] contrasts in limma and missing values
Hans-Ulrich Klein
h.klein at uni-muenster.de
Mon Oct 29 19:42:27 CET 2007
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
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