Hi everyone, I am stuck with creating design matrix in LIMMA for my microarray experimental design. The experiment consists of 40 Agilent arrays. The subjects were treated with two stress conditions (S1 and S2). In each stress condition, the subjects were sampled in 5 timepoints (0, 6, 12, 24 and 48). Microarray experiment was performed in such a way that every fourth array of a particular timepoint, irrespective of stress treatment, is dye swapped. Basically, it is a time course experiment on the same subject with two different stresses. I want to to know which are the genes important/responsible for stress 1 or 2. The target file looks like below:

```
SampleNumber FileName Cy3 Cy5 Stress
1 Array1 pool1 S1_Time0 S1
2 Array2 pool1 S1_Time0 S1
3 Array3 pool1 S1_Time0 S1
4 Array4 S1_Time0 pool1 S1
5 Array5 pool1 S1_Time6 S1
6 Array6 pool1 S1_Time6 S1
7 Array7 pool1 S1_Time6 S1
8 Array8 S1_Time6 pool1 S1
9 Array9 pool1 S1_Time12 S1
10 Array10 pool1 S1_Time12 S1
11 Array11 pool1 S1_Time12 S1
12 Array12 S1_Time12 pool1 S1
13 Array13 pool1 S1_Time24 S1
14 Array14 pool1 S1_Time24 S1
15 Array15 pool1 S1_Time24 S1
16 Array16 S1_Time24 pool1 S1
17 Array17 pool1 S1_Time48 S1
18 Array18 pool1 S1_Time48 S1
19 Array19 pool1 S1_Time48 S1
20 Array20 S1_Time48 pool1 S1
21 Array21 pool2 S2_Time0 S2
22 Array22 pool2 S2_Time0 S2
23 Array23 pool2 S2_Time0 S2
24 Array24 S2_Time0 pool2 S2
25 Array25 pool2 S2_Time6 S2
26 Array26 pool2 S2_Time6 S2
27 Array27 pool2 S2_Time6 S2
28 Array28 S2_Time6 pool2 S2
29 Array29 pool2 S2_Time12 S2
30 Array30 pool2 S2_Time12 S2
31 Array31 pool2 S2_Time12 S2
32 Array32 S2_Time12 pool2 S2
33 Array33 pool2 S2_Time24 S2
34 Array34 pool2 S2_Time24 S2
35 Array35 pool2 S2_Time24 S2
36 Array36 S2_Time24 pool2 S2
37 Array37 pool2 S2_Time48 S2
38 Array38 pool2 S2_Time48 S2
39 Array39 pool2 S2_Time48 S2
40 Array40 S2_Time48 pool2 S2
```