Thanks for the Diffbind package, it makes DB analysis very easy.
However, I have the following question: How does DiffBind handle Input samples and how does it compare condition B with condition A? For example, I have a experiment design like this:
Condition A B IP 2 2 IN 2 2
The number 2 indicates 2 biological replicates for each cell.
When DiffBind calls DESeq2, what contrast does it use internally to calculate LFC and FDR between condition A and B?
1. A_IP - B_IP 2. (A_IP - A_IN) - (B_IP - B_IN) 3. sth. else?