Dear Bioconductor community,
I have a two-way experiment in which time course profiles are to be compared for two many groups.
The two experimental dimensions or factors here are Treatment (A-D-F) and Time. For covenience, as explain in Limma user manual, I used a combinaison of Treatment/Time = Group in the target frame.
Animals received different treatment (A, D or F). But for some reasons some samples are missing in some groupes
Should I use a blocked model on animals or is it a problem ?
I want to identify :
1/ Which genes respond at either the Day1, Day3 or Day27 in the different group ( and D1, D5 , D7 for Group F)
2/ Which genes respond differently over time in the different groups (D3, D7, Day 27/28)
The results for gene set enrichment analysis I obtained for comparison over time in Group F perplex me. This is why I'm wondering if my analysis is right.
Thanks in advance for your help