[BioC] edgeR: design matrix for different condition

[KJ Lim]

Dear the edgeR community,

Good day.

I'm analyzing my RNA-Seq experiment with edgeR. My study has 2
different genotypes (treeHS, treeLS) and time of treatment (0H, 3H,
24H, 96H).

I first assumed that the treatment effect will be the same for each
genotype and I have the design matrix as:

  design <- model.matrix(~tree+treat)

> design
   (Intercept)  treat03H  treat24H  treat96H  treeLS
1             1        0        0        0      0
2             1        0        0        0      0
3             1        1        0        0      0
4             1        1        0        0      0
5             1        0        1        0      0
6             1        0        1        0      0
7             1        0        0        1      0
8             1        0        0        1      0
9             1        0        0        0      1
10           1        0        0        0      1
11           1        1        0        0      1
12           1        1        0        0      1
13           1        0        1        0      1
14           1        0        1        0      1
15           1        0        0        1      1
16           1        0        0        1      1

I used coef=4 to test for the differential expressions between treeHS
and treeLS within the time of treatment, coef=3 to learn the
differential expressions in 2 genotypes at time of treatment 96H.

** I would like to learn the genes are express in treeHS but not
treeLS and vice versa at certain time of treatment let's say 24H or
across the whole time of treatment, should I have the design matrix as
below or more steps I need to do?

  design <- model.matrix(~tree*treat)

Kindly please light me on this. I appreciate very much for your help and time.

Have a nice day.

Best regards,
KJ Lim