would appreciate a suggestion please : considering a replicated experiment comparing Normal vs Tumor :
Normal1 Normal2 Tumor1 Tumor2
when setting up the list of samples for differential analysis in edgeR,
group <- factor(c("normal","normal","tumor", "tumor"))
y <- DGEList(counts=x,group=group)
y <- calcNormFactors(y)
y <- estimateCommonDisp(y)
how could I indicate that Normal1 is paired with Tumor1, and Normal2 is paired with Tumor2 ? thank you !