I have a data set where I am comparing a few exposures to a basleine group. When I run Deseq on all of the groups it filters out about 20,000 of the 36,000 genes which is what I expect and has always been the case when running Deseq. However, for 1 of the contrasts only 200 genes get filtered out. Looking at the results table it looks like almost 15,000 genes that make it through have counts < 1. Does anyone know why the low counts filter would not be filtering here?
out of 35599 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up) : 0, 0%
LFC < 0 (down) : 0, 0%
outliers  : 0, 0%
low counts  : 205, 0.58%
(mean count < 0)
 see 'cooksCutoff' argument of ?results
 see 'independentFiltering' argument of ?results
 "Genes < 0.05:"