I used the glmQLFTest function by edgeR to detect differentially expressed genes. I have ONE dataset and two gene lists: (1) all genes (2) genes remained after removing lowly expressed genes by filterByExpr
In the result table, I found that logFC and logCPM for each gene remained unchanged between (1) and (2), which is as expected. However, the F statistic changed, tend to be decrease, for some genes.
As a result, genes identified as significant (FDR < 0.05) in (1) would become in-significant in (2).
Dose this make sense? Thanks in advance!