hello, I have a time-series, two factor design that I would like to analyze with DESeq2. The factor levels are: Genotype (wt, mut) Tissue_age (old, young) Time (pretreat, treat1d, treat4d, post-treat) The design is balanced with same number of bio reps per treatment (n=3). Each rep was collected from individual experiments, meaning the samples were not collected in the same experiment. Leaf age is nested within genotype, since the tissue (old and young) was collected from the same plant in each bio rep. Q1.Should I include the reps as a factor since they're derived from individual experiments? from the PCA they all group very nicely together.
Q2. Based on PCA analysis I see that tissue_age effects are evident during treatment(1d and 4d), while genotype effects are specific to posttreat responses. So, the interactions tissue_age:time and genotype:time are very important for me as it's also the tissue_age:genotype:time interaction. I think I have a good idea about the contrasts I'd need to do, however I am not sure how to write the design(s) to do the contrasts I want to do. How would the formula look like. Any suggestions will be highly appreciated.
Thank you.
