I am just seeking confirmation about likely relationship between the
baseMean and the
mean of normalised counts measured in DESeq2. Thing is at the beginning of my analysis I use to filter genes with low counts
despite this I still have in my gene list and thus in my MA plot genes with baseMean <1. I know that the
mean of normalised counts is the average expression between compared groups whereas the baseMean is a just the average of the normalised count values, dividing by size factors. So there should be a relationship between those values, I guess?
Could it be that they successfully passed the shrinkage due to very high log2foldchange?