Hello, I have a set of RNA seq data from a clinical trial with 2 treatment groups (active (n~90 pts), placebo (n~35 pts) and each patient has 2 RNA samples (pre and post treatment). I plan to use limma with the voom transformation for analysis to detect DEG between the two groups. Can someone provide guidanance or suggestions on non-specific filtering criteria to filter low expressed genes and the rationale behind a chosen cutoff? My understanding is the data need to be normalized and the voom exptects the lowly expressed genes to be removed for the weight calculations. I've tried a few available tools and suggested methods but would like help choosing a methodology for cutoff selection(s) for this design.