I'm Andrea and i'm a student. Currently, I'm work on phosphoproteomic data collected in an excel file. In particular, i have in each row the expression levels of gene for mutant and wild-type condition, 3 replicas for each condition (six columns: M1 M2 M3 WT1 WT2 WT3 - exe: gene1: M1 M2 M3 WT1 WT2 WT3). I have a question on the design matrix because i'm not sure i did well. This is my design matrix:
## Design Matrix samples = factor(c(rep("M", each = 3), rep("WT", each = 3))) design = model.matrix(~ 0+samples) colnames(design) = levels(samples) rownames(design) = colnames(Data) design > design M WT M1 1 0 M2 1 0 M3 1 0 WT1 0 1 WT2 0 1 WT3 0 1 attr(,"assign")  1 1 attr(,"contrasts") attr(,"contrasts")$samples  "contr.treatment"
Is it correct? Please, someone could help me? Thanks, Andrea.