Hi, I have a question about evaluating dye effects in limma. In chapter 8.1.2 of limma users guide, an example is given to demonstrate how to estimate dye effects. The design matrix is constructed by the following command: >design <- cbind(DyeEffect=1,MUvsWT=c(1,-1,1,-1)) > design DyeEffect MUvsWT [1,] 1 1 [2,] 1 -1 [3,] 1 1 [4,] 1 -1 In my case, I ignored the dye effects previously. Now I want to correct the dye effect. I am wondering how to build the design matrix. According to the above-mentioned example, I think adding one column (DyeEffect=1) to my previous design matrix will do. Is that right? > design <- cbind(DyeEffect=1,design) Thanks! Dejian