I am using edgeR to do differential gene expression analysis on my mRNA seq data.
I just have two group, each of 5 replicates, that I want to compare.
Out of curiosity I performed both the classic EdgeR (exact test) and the GLM (glmQlFtest) approaches.
Surprisingly, I got really different results, the exact test gave me 192 upregulated genes but the GLM approach only 82.
Is it normal to get such big differences between the two methods?
Which test is preferred for a simple design like this?