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