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.