[R] edgeR Time Series

[rmje]

I have a time serie of 10 time points, including Treated and Control samples.
In total my data contains 20 columns.
I have grouped Treated and Control samples into 3 categories, Early, mid and
late. I want to compare The early  Treated Group with the early Control
group, The mid Treated with the mid Control and so on...

Is this the correct way of making a design matrix? I am uncertain about the
results I get.

> Time <-
> factor(c("Early","Early","Early","Early","Mid","Mid","Late","Late","Late","Late","Early","Early","Early","Early","Mid","Mid","Late","Late","Late","Late"))
> Condition <-
> factor(c("T","T","T","T","T","T","T","T","T","T","C","C","C","C","C","C","C","C","C","C"))
> data.frame(Sample=colnames(y),Time,Condition)
   Sample  Time Condition
1     T0h Early         T
2  T0.25h Early         T
3   T0.5h Early         T
4     T1h Early         T
5     T2h   Mid         T
6     T3h   Mid         T
7     T6h  Late         T
8    T12h  Late         T
9    T24h  Late         T
10   T48h  Late         T
11    C0h Early         C
12 C0.25h Early         C
13  C0.5h Early         C
14    C1h Early         C
15    C2h   Mid         C
16    C3h   Mid         C
17    C6h  Late         C
18   C12h  Late         C
19   C24h  Late         C
20   C48h  Late         C

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