I am new to using DEseq2 and multiple factor design. I have gone through forum discussions that deal with DEseq2 and multifactorial designs. However, I would like to understand if my design for the following matrix is correct?
That is we have 3 cell types for each condition (knock out (KO) and wild type(WT)). I would like to perform teh following differential analysis
1. For KO condition, I would like to perform a comparision between each cell type
2. For each cell type, I would like to compare between KO and WT
Should I set up the design as follows? ~CellType+CellType:Condition
Thank you in advance and any pointers or help is appreciated.