Hi, I am using limma to do a multiple group analysis using Affymatrix data. I am trying to perform analysis for 12 samples which are from control (C) and disease (D) group and these are either treated with drug (S) or not (N). The replicas are not consistence across the group. I run the following code:
types <- factor(types, levels=c("C.S","C.N","D.S","D.N")) design <- model.matrix(~ 0+types) colnames(design) <- levels(types) contrast.matrix <- makeContrasts(C.SvsN=C.S-C.N, + D.SvsN=D.S-D.N, + Diff=(D.S-D.N)-(C.S-C.N), + levels=design)
But when I run the below code
fit <- lmFit(exprs(eset),design)
I get the error message:
"Coefficients not estimable: C.N D.N " "Error in lm.fit(design, t(M)) : incompatible dimensions"
I will really appreciate if someone can help me to understand this error and help me to debug this problem.