I have RNAseq with multiple factors such as 4 genotypes, 2 treatment and 4 time points. The top few lines look like,
Samples Genotype Treatment Time S1 VN1 Control 1hr S2 VN1 Control 1hr S3 VN1 Stress 1hr S4 VN1 Stress 1hr S5 VN1 Control 3hr S6 VN1 Control 3hr S7 VN1 Stress 3hr S8 VN1 Stress 3hr . .
Now I am estimating DEGs using DESeq2 package. My intention is to make pairwise comparisons to see time effect and treatment effect using different combinations. For example,
VN1 at 1hr in Control Vs VN1 at 1hr in Stress VN1 at 1hr in Control Vs VN1 at 3hr in Control
Since the experimental setup includes multiple factor,I am a bit confused about the correct design for my purpose. Can anyone help?