I have this paired experiment: control (16) and treated (17) groups, each was submitted to SD and HF diet.
1) I want to know the effect of SD in control samples?
count matrix contains control samples only and design = ~ subject.n + Diet where subject.n is the samples origin (patient id:1,1, 2,2..) Shall I add any interaction term to answer this question?
2) I want to know the effect of SD in treated samples?
count matrix contains treated samples only and design similar to the previous. similarly should I include any interaction term?
3) I want to know the DEG between the treated and the control samples?
should i remove the unpaired treated sample? what shall be the design in this case?
design~ condition + diet + subject.n but what should be the interaction terms?
Thank you for your help.