[BioC] desing matrix and interaction term difficulty

[Brian [guest]]

Dear Dr.Smyth and Limma users;

Good morning.
I have an experiment which has 4 variables; sham surgery, full surgery, treatment 1 and treatment 2. I am having difficulty formulating a design matrix and interaction terms for this experiment.  Treatment 1 is known to us and treatment 2 is the novel therapeutic.

Groups are as follows:
sham + treatment1
sham + treatment2
full + treatment1
full + treatment2

I need to answer:
* gene exp difference between treat1 and treat2 in both models sham and full in order to verify full surgery working, and to prove treatment 2 is working to protect animal from full surgery detriments.  Treatment1 is considered a known drug with known effects.

I am also confused (or ignorant) on how to employ a proper "difference of difference" or interaction term.

I greatly appreciate any help and understand and respect everyone's time constraints.
Thank you,
Brian

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