I have collected two types of kidney tissues - normal and disease. I have 3 biological replicates. RNA seq is done for this set up. I am stuck with the data analysis. I want to compare normal vs disease kidney tissue. When I think of averaging biological replicates for each tissue types, I find it a bit problematic because I want to capture the differentially expression gene data between the different tissue types in a biological replicates.
Additionally, organs in different humans are bound to be different due to various factors. Furthermore, I also want to compare the normal tissue of different biological replicates.
Any suggestion please?