Hi,

I have 16 samples and multiple conditions (treatment and sex):  (4 Untreated_male, 4 Untreated_female, 4 Treated_male, 4 Treated_female)

I want to do 3 types of DEG analysis using DESeq2.  

1. Treated_female VS Untreated Female
2. Treated_male VS Untreated male
3. Treated VS Untreated controlled by sex

I am very new to DESeq2. I read in some posts that for the #1 and #2 analysis, it is better to combine all the 16 samples in dds and then set a design just specifically for Treated_female VS Untreated Female. 

I know that:

`design= ~ treatment`      ( will result in untreated VS treated (both sexes))

`design= ~ sex+treatment+sex:treatment`  ( will result in Treated VS Untreated controlled by sex)

but how about the #1 and #2 analysis? how can I specify the design for just one sex?
I think that the first 2 analyses, the 8 samples of the other sex are not relevant and so need not be combined. Also, I think you mean you have 16 samples, not 12.

You can create 3 DESeq datasets, one with all male samples and `design = ~ treatment`, one with all female samples and same design, and the third with all 16 samples and a combined formula. I don't understand why the design formula has the `sex:treatment` term though - how does that change a design of just `sex + treatment`?