I have started using DESEQ2 package recently for RNA-Seq analysis. I observed that a lot of genes in my list had been assigned a missing value (NA). On reading further, I noticed it can be avoided by taking care of the cooksCutoff and independentFiltering, i.e. cooksCutoff = FALSE, independentFiltering = FALSE.
However, even after that, I found almost 3000 genes which had an NA value assigned to my gene list. Is there any other way to prevent the missing values from occurring at all? If not, how can I proceed further?