I have a question about creating the "design formula" for my linear model within edgeR.
First I will explain the experimental design:
7 subjects donated tissue samples.
For each donor, their tissue was separated in 4 groups (n = 28):
- 1st group was stimulated with an enzyme for 5 days.
- 2nd group was stimulated with the same enzyme for 10 days
- 3rd group was a mock-treatment control group for 5 days
- 4th group was a mock-treatment control group for 10 days
The top of the design matrix looks like this:
sample treatment time
sample1 enzyme 5.day
sample1 mock 5.day
sample1 enzyme 10.day
sample1 mock 10.day
sample2 enzyme 5.day
sample2 mock 5.day
My design formula looks like this:
But I'm not sure it is correct...
The main question we're asking is:
1.) Which genes are differentially expressed between treatment (enzyme stimulation) and control?
2.) does 10 day stimulation significantly differ from 5 day stimulation, when compared to control?
p.s. I will actually upvote your answer if you help me solve this :D