I am having a query related to VOOM function in the limma package. I am trying to analyze proteomics data using limma to identify the differential expression between two groups which has control(n=3and tumor, n=6). There is only biological replicates and not any technical ones. I have a doubt that the matrix design is correct or not . Also limma can be used for the analysis proteomics data obtained from masspectrometry platform .
design <- model.matrix(~ -1 + > factor(c(1,1,1,1,1,1,2,2,2)))
design <- model.matrix(~-1 + factor(rep(1:2, 1=6,2=3)))
colnames(design) <- c("tumor","control") contrast <- makeContrasts(tumor - control, levels = design)
voom(counts, design = NULL, lib.size = NULL, normalize.method = "none", span = 0.5, plot = FALSE, save.plot = FALSE)