Dear R-users,

I am facing a problem in constructing design matrix. My data is qPCR data,
analysing 92  protein markers in 92 samples (two groups). I would like to
use Limma package to identify differently expressed genes between two
groups. The first 38 samples were controls, and the other 54 samples were
cases. So how should I construct the design matrix.

I have tried the following code. Is this right?
design<-matrix(rep(1,184),nrow=92,byrow=TRUE)
design[39:92,1]=0
design[1:38,2]=0
colnames(design2)<-c("control","case")

Could anyone help me figure out it? Thank you.

Adam

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