I am a novice for R and bioinfomatics. I am trying to run DESeq2 with my raw count table (.txt). I have been trying to follow the beginner's guide for the DESeq2 package, but it is still hard to understand because my experimental condition is different from the example. Would you please help me to figure it out how to make a DESeqDataset and run? Thank you in advance for your time.
Here is my experiemtal design.
- Treatment: Control vs Treated
- Animal group: 4 genotypes in duplicate (genotype1-1, genotype1-2, genotype2-1, genotype2-2, genotype3-1, genotype3-2, genotype4-1, genotype4-2)
- Model: Treatment, Animal group, Aniaml * Treatment (interaction of animal and treatment).
I want to run DESeq2 with 2-way ANOVA-like frame work (2 treatment X 4 genotypes).