I have two samples under 2 different conditions. I would like to use edgeR to do DEG analysis between these 2 samples. I have read the edgeR manual and I know that if we have 2 or more biological replicates in both conditions we can use glmQLFit(). Or if we don't have biological replicates for our samples in experiment we can use exactTest() and manually set the dispersion.
Now I am dealing with the case that my sample1 has 2 biological replicates and sample2 is only one replicate. I want to compare these 2 samples to do DEG analysis. I went over the edgeR manual but I could not find such case being explained.
Do you have any idea how can I handle this?