Is this the correct design matrix for the following experiment? The experiment has a Normal cell line (P) and a Mutant cell line (X) that were grown with decreasing nutrient levels, A, B, and C. A is represent 100% nutrient for a particular component, B represent 50% , and C represents 0%. The Normal cells (P) could only grow in A and B, while the Mutant cells (X) could be grown in A, B, and C. The objective is of the study was to identify gene expression levels that changed (i.e., gene sensitive to the nutrient) that allowed the mutant to grow without the nutrient.
celltype <- factor(samples$ct, levels = c("P", "X"))
trt <- factor(samples$trt, levels= c("A", "B", "C"))
design <- model.matrix(~0+celltype+trt)
rownames(design) <- samples$file
# "celltypeP" "celltypeX" "trtB" "trtC"