Creating design matrix in LIMMA

Question

[sgblackpearl]

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

Answer 1

[apa@stowers]

I want to ask -- why are you still doing arrays?? :)

If I understand the experiment correctly, below is the design matrix that I think I would use. It's been a while, though. And there are multiple ways to describe the matrix, depending on what kind of linear model you want.

You might read the LIMMA User's Guide Chapter 8, which talks about design matrices.

Num T0  T6  T12 T24 T48 S1  S2
1   1   0   0   0   0   1   0
2   1   0   0   0   0   1   0
3   1   0   0   0   0   1   0
4   -1  0   0   0   0   1   0
5   0   1   0   0   0   1   0
6   0   1   0   0   0   1   0
7   0   1   0   0   0   1   0
8   0   -1  0   0   0   1   0
9   0   0   1   0   0   1   0
10  0   0   1   0   0   1   0
11  0   0   1   0   0   1   0
12  0   0   -1  0   0   1   0
13  0   0   0   1   0   1   0
14  0   0   0   1   0   1   0
15  0   0   0   1   0   1   0
16  0   0   0   -1  0   1   0
17  0   0   0   0   1   1   0
18  0   0   0   0   1   1   0
19  0   0   0   0   1   1   0
20  0   0   0   0   -1  1   0
21  1   0   0   0   0   0   1
22  1   0   0   0   0   0   1
23  1   0   0   0   0   0   1
24  -1  0   0   0   0   0   1
25  0   1   0   0   0   0   1
26  0   1   0   0   0   0   1
27  0   1   0   0   0   0   1
28  0   -1  0   0   0   0   1
29  0   0   1   0   0   0   1
30  0   0   1   0   0   0   1
31  0   0   1   0   0   0   1
32  0   0   -1  0   0   0   1
33  0   0   0   1   0   0   1
34  0   0   0   1   0   0   1
35  0   0   0   1   0   0   1
36  0   0   0   -1  0   0   1
37  0   0   0   0   1   0   1
38  0   0   0   0   1   0   1
39  0   0   0   0   1   0   1
40  0   0   0   0   -1  0   1