I have roughly 100 samples (2 groups) of noisy human tissue data. Thinking about filtering to improve the multiple testing situation. Thus far, I filter by cpm values (calculated using edgeR after counting with featurecounts), and run voom/limma afterwards. I have also stumbled over htsfilter, and thought about variance filtering.
Now I heard that filtering, at least by variance or htsfilter, was per se incompatible with limma or other empirial Bayes methods.
What do you experts think/suggest?