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I am trying to construct my design matrix needed in the {limma} function "lmfit" but am having trouble with the formula I am to specify in the function "model.matrix". Namely when to I use ~0 + factors (ex 1) vs ~-1 + factors (ex 2). Any clarification on this would be greatly appreciated. Thanks in advanced.
Ex 1:
f <- factor(targets$Target, levels=c("RNA1","RNA2","RNA3"))
design <- model.matrix(~0+f)
[page 409, of Bioinformatics and computational biology solutions using R and Bioconductor]
and
Ex 2:
library(ALL)
pdat <- pData(ALL)
design <- model.matrix(~-1 + factor(pdat$type)
[page 237, of Bioinformatics and computational biology solutions using R and Bioconductor]
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