Hi,
I have a question about an analysis of RNA seq data via DESeq2.
The RNA seq design is the following:
Sample experiment siRNA hormonal treatment
1 M0 sineg control
2 M1 sineg control
3 M2 sineg control
4 M0 sineg hormone
5 M1 sineg hormone
6 M2 sineg hormone
7 M0 siX control
8 M1 siX control
9 M2 siX control
10 M0 siX hormone
11 M1 siX hormone
12 M2 siX hormone
So there are two conditions (siRNA and hormonal treatment) and within each condition there are a control sample (sineg or control) and a treated sample (siX or hormone). And we realized 3 experiments (M0,M1,M2).
I would like to identify genes that respond differently to hormonal treatment in condition siX compared to the condition sineg. The design I used is the following: ~ hormonal treatment + si + hormonal treatment :si. Is it OK?
Finally I would like to take into account the experiment. In fact my experiments are paired. For example, a treatment for the experiment M0 must be compared with the control of the same experiment M0. So my question is: how do I set up the design for that?
Thanks in advance.
Severine

