Hi,

I have a question related to the multifactor formula design:

In my experiment, there are 12 rats with 3 genotypes. For each rat, 4 tissues from different brain areas were isolated.

Eat Genotype TissueArea 1 Hom Prefrontal cortex 1 Hom Cerebellum 1 Hom Corpus callosum 1 Hom Hippocampus 2 Het Prefrontal cortex 2 Het Cerebellum 2 Het Corpus callosum 2 Het Hippocampus . . .

My scientific question is the difference among 3 genotypes. So the formula should be design = ~ TissueArea + Genotype.

What if I want to look specific tissue area? Like the influence of genotype in the prefrontal cortex. Can I subset the data for the prefrontal cortex and perform DESeq separately?

Thank you for your help in advance!

Yes. Concatenate the tissue and genotype names into one factor, and then fit a cell means model on that. You can then make contrasts between any combinations of tissue and genotype that you like.