I'm confused about how to identify differentially expressed genes (DEGs) in a single-channel expt.
Is it possible to identify DEGs without making a contrast.matrix?
I saw examples just did:
fit <- lmFit(...)
fit <- eBayes(fit)
tt <- topTable(fit, coef=2)
All DEGs are stored in tt
However, when I looked up the limma user guide (version 2016) in section 9.6, the example used contrast.matrix.
Can someone help?