I have some bulk RNA-Seq data obtained from exposing cells from a cell line to 5 different treatments (A, B, C, D and E), along with a medium-only control. This experiment was repeated 5 times (on different passages of the cells, with 1 experiment per week). I am interested in generated lists of DEGs for each treatment vs control (i.e. A vs Ctrl, B vs Ctrl etc...).
I have generated said lists of DEGs using various different experimental designs described in the edgeR Users Guide:
- Grouped - where design = model.matrix(~0+Treatment)
- Paired - where design = model.matrix(~Replicate+Treatment)
- Paired (with blocking) - where design also = model.matrix(~Replicate+Treatment)
Where Treatment is either Ctrl, A, B, C, D, or E and Replicate is a number 1-5.
I find that the paired design is much more stringent than the paired design with blocking (~half the number of DEGs). Could somebody please suggest which is most suitable for my use case?
Thanks in advance!