
Hello, when I create a design of a matrix with:

 cond <- factor (rep (1:4, EACH = 2))   # 2 replicates of each treatment
  design <- model.matrix (~ 0 + cond)

  colname (design) <- c ("treatment1", "treatment2", "treatment3", "treatment4")

  contrast <- makeContrasts (treatment2-treatment1, treatment3-treatment1, treatment4-treatment1, Levels = design)

 How bioconductor knows the treatment1, treatment2, treatment3 and treatment4? Files must be loaded in any particular order?

Thanks,
Paz
 		 	   		  
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