I have a RNA seq data which I am trying to identify DEGs. Dataset contains three sets of Untreated - 2 replicates and Treated - 2 replicates. My DEseq2 results shows padj values NA and some p values and padj values as zero. A total of 3000 genes shows such result.

I tried using res <- results(dds, independentFiltering = F) and res <- results(dds, cooksCutoff=FALSE) but I am unable to understand what difference both of these filtering makes

Is it good to use independentFiltering = F or cooksCutoff=FALSE for 3000 genes which shows padj values NA and some p values and padj values as zero

Can anyone please help me how to solve this.

The mechanism that sets adjusted p-values or p-values to NA is listed in the FAQ:

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-are-some-p-values-set-to-na