Dear community, I have a short question regarding the independent filtering of p values. I understand that it filters out genes with low baseMean irrespective of the biological condition, but in my results, I have three different contrasts, and for many genes, only the padj of one of them was set to NA while the contrasts obviously all have the same baseMean for the same gene. All three contrasts have a valid p-value so the NA is not from the outliers. So why is the NA only applied to one of the comparisons if the filter doesn't consider biological conditions?

Thanks!

See the vignette section on NA values.