Hi all,

I'm in the process of analysing my RNASeq data and had a couple of question about setting up the model matrix to get the comparisons I want. 

First of all my experimental setup is looking at genes that respond to diet in males and females. 
> Protein-Female
> Carbohydrate-Female
> Protein-Male
>Carbohydrate-Male

the model matrix I have setup is:
> des1

   Fem.P Male.P Fem.C Male.C
1      1      0     0      0
2      1      0     0      0
3      1      0     0      0
4      0      1     0      0
5      0      1     0      0
6      0      0     1      0
7      0      0     1      0
8      0      0     1      0
9      0      0     0      1
10     0      0     0      1
11     0      0     0      1

 to look at differences between the diets within each sex I have done the contrast:

FemC-FemP and MaleC-MaleP in separate analyses. 

I am interested in finding out the genes that do different things in males and females in response to diet (sex x diet interaction)
What contrast do I do to get to this question? 
I was thinking something like:
makeContrast((Fem.C-Fem.P)-(Male.C-Male.P), level=des1)

is this correct?

thanks!!

Yes, that's correct. Your last contrast will identify the difference in the diet effects between sexes, i.e., the interaction between diet and sex. If no interaction existed, sex and diet should be purely additive, such that the effect of diet in females (Fem.C - Fem.P) should be the same as that in males (Male.C - Male.P).

Note that interpretation of the interaction often requires that you report the individual diet effects in both sexes as well, just to see whether the interaction is due to decreased/opposite/elevated effect in males relative to females.