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.
- Treated_female VS Untreated Female
- Treated_male VS Untreated male
- 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?