I am reading Smyth et al. (ref. 1). I want to run differential expression analysis on a bulk RNA-Seq dataset in which each group is composed by 2 samples. In the paper previously cited it is written that:
Genes must be expressed in at least one group (or in at least three samples across the entire experiment, where three was chosen as this is the smallest group size) to be kept for downstream analysis.
Is it possible to use limma DE analysis also with groups composed by only 2 samples? NB. It is possible that in this particular dataset the smallest group size is 3.
If not, which alternative should I use?
I have 17 samples. My idea is to test one group vs the rest of groups (all together). So at least the reference group would be composed by > 10 samples. In this case, what can be a feasible analysis for DE?
- Smyth, G. K., Law, C. W., Alhamdoosh, M., Su, S. & Ritchie, M. E. RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR. F1000Research 5, 1408 (2016).