I have a DeSeq2 logfold change output file for sample 1 vs sample 2 I am comparing with the following columns below:
"Loci" "baseMean" "log2FoldChange" "lfcSE" "stat" "pvalue" "padj"
I understand that I can extract differentially expressed loci from the table above using padj threshold of <0.1 significance. Can someone please tell me how I can separate **upregulated genes**, **downregulated genes** and gene sets with **no difference (i.e conserved loci)**. What are the cutoff values I should be considering (specifically for
padj) if I need to extract each of these gene subsets (i.e upregulated genes, downregulated genes and gene sets with no difference (i.e conserved loci)? Also, I have lots of loci with
NA's and I want to know what
NA's mean in this case.