Hi all,

I have done a paired analysis (VTE1 vs VTE0 + pair) on RNA-Seq data and an unpaired analysis (VTE1 vs VTE0) using EdgeR. I noticed that there is a difference in Log2FC values in the 2 analysis. This is probably caused due to difference in the design (I guess). My samples look like this:

Samples VTE pair
sample1 0   pair_1
sample2 1   pair_1
sample3 0   pair_2
sample4 1   pair_2
sample5 0   pair_3
sample6 1   pair_3

In case of the unpaired analysis fold changes are calculated by log2(mean(VTE1)/mean(VTE0)). However, I have no idea how the FC values are calculated when adding the pairs to it.

Hope my question is clear and someone can explain this to me!

Best regards, Tom