Design matrix for limma

Question

[hakimelakhrass]

Hello, I am new to microarray data and I am looking to make a design matrix. Following the limma documentation I made the following design matrix:

control controlvstreatment
 [1,]       1                  0
 [2,]       1                  0
 [3,]       1                  0
 [4,]       1                  0
 [5,]       1                  0
 [6,]       1                  0
 [7,]       1                  0
 [8,]       1                  0
 [9,]       1                  0
[10,]       1                  0
[11,]       1                  0
[12,]       1                  0
[13,]       1                  0
[14,]       1                  1
[15,]       1                  1
[16,]       1                  1
[17,]       1                  1
[18,]       1                  1
[19,]       1                  1
[20,]       1                  1
[21,]       1                  1
[22,]       1                  1
[23,]       1                  1
[24,]       1                  1
[25,]       1                  1
[26,]       1                  1

My results came out like this:

  control controlvstreatment
-1       0                517
0        0              25892
1    26806                397

Which look a little weird. Now I need to expand to 5 time points and I am not sure how. Thanks in advanced.

[Devon Ryan]

I'm not sure what looks so weird about those results. The "control" column is the intercept, so you can ignore it. How to deal with multiple time points depends on the question(s) you want to ask.

[hakimelakhrass]

Ah I see now. I am trying to find the DEGS between all time points. I am not sure exactly how to go about it. I have a baseline two time points in the middle and a time point that acts as an "after".

[Devon Ryan]

So you presumably want most of the pairwise comparisons. Generally you would use a model like ~0+timepoint and use a bunch of contrasts, one for each comparisons you want to make.