I have a question about the genes that get Padj = NA.
In my experiment I compare 3 control samples and 3 treated samples. Out of 4500 genes, about 1800 get Padj = NA. I wish to understand how to treat these genes: as not changed genes or to exclude them from my analysis. Since I want to do a Fisher test on the data it is important for me to know for each gene if it changed, did not change or undetermined.
As I understand from the vignette this happens because of the automatic independent filtering. I read in section 3.8 that this is an optimization of the FDR correction (optimizing the number of genes which will have an adjusted p value below a given FDR cutoff, alpha).
I also read that it is possible to remove the independent filtering by writing independentFiltering=FALSE in the results function.
My question is how to treat these Padj=NA genes and what do I lose if I run DEseq2 without the independent filtering?
Thank you very much,
Raya Romm, PhD student
The Hebrew University of Jerusalem