Hi

I am trying to analyse an agilent two-color dataset with a direct experimental design (no reference). It consists of paired (treated and untreated samples) for each time point hybridized to a single array. The data is in two cell lines (denoted as M & P). I am trying to construct a design matrix.I am fairly new to Limma/R and am still struggling after hours of searching. Any help would be appreciated.

Here are my samples:

Name Cy3 Cy5

M_day7 M_mock_day7 M_trt_day7

M_day10 M_mock_day10 M_trt_day10

P_day7 P_mock_day7 P_trt_day7

P_day10 P_mock_day10 P_trt_day10

Thanks!

For the second and fourth arrays, you have the same mock group for both dyes. Is this actually the case?

Thanks for pointing it out. Sorry for the confusion. I have edited my post.