I have some doubts about the differences of the following interaction models:
~ind+grp+cnd+grp:cnd ~grp+grp:ind+grp:cnd ~grp+cnd+grp:ind+grp:cnd
After reading the DESeq2 manual and forums I still did not understand the differences.
My experiment design is:
GROUP CONDITION ind.n s1 CONTROL no_treat p1 s2 CONTROL no_treat p2 s3 CONTROL no_treat p3 s4 CONTROL treat p1 s5 CONTROL treat p2 s6 CONTROL treat p3 s7 KO no_treat p2 s8 KO no_treat p3 s9 KO no_treat p1 s10 KO treat p2 s11 KO treat p3 s12 KO treat p1
And I would like to know the differential response of the treatment between groups accounting for the patient effect.