I have ChIP-seq datasets as the following:
I would like to find differential region of pulldown between WT and MT in condition after controlling individual cells and types. I thought the design formula: ~ Cell + Type + Condition + Type*Condition. However, it generated "not full rank" error. When I tried to nested formula such as ~ Cell + Cell*Type + Cell *Condition, it still generated "not full rank" error. It only works with ~ Type + Condition + Type*Condition where I cannot block cell effect. Could anyone help me?