I want to analyze RNA_Seq data that I found on the internet to practice. I found 8 RNA_Seq datasets (four different immune cells from mice and everytime two biological replicates). The goal of the analysis is to discover if there are genes that are differentially expressed.
I want to used edgeR to analyze the data. In order to order to do that, I need to specify a design matrix. There I am stuck. Cell type is one factor with 4 different levels in this analysis, but what about biological replicate? Should it also get an own factor with two levels?
I think biological replicate should not get a own factor, but I can not really explain why. It is a hunch.
Thanks in advance.