**0**wrote:

Hi all

I've been unsuccesfully browsing forums, limma user guide to find an answer to the following question, I know there are many posts on this allready, so forgive me mine:

We performed following experiment: we infected a celline with a virus and extracted RNA at 4 timepoints after infection. These 4 timepoints are paired to an uninfected condition. This experiment was performed twice to reach 16 samples in total for array analysis.

```
experiment time treatment
1 1 2h uninf
2 1 6h uninf
3 1 18h uninf
4 1 30h uninf
5 1 2h inf
6 1 6h inf
7 1 18h inf
8 1 30h inf
9 2 2h uninf
10 2 6h uninf
11 2 18h uninf
12 2 30h uninf
13 2 2h inf
14 2 6h inf
15 2 18h inf
16 2 30h inf
```

I am trying to get differential expression at the individual timepoints (2 pairs of uninf vs inf) but creating the correct design matrix to account for paired samples doesn't work for me yet.

Any advice would be more than welcome to provide the correct design and contrast matrix.

Greetings

Wim