I used DESeq package to analyze my RNA-seq data but I have a problem regarding filtering. I have only one replicate for each sample (therefore I used method="blind", sharingMode="fit-only"))
The problem is that all padj values are 1, there are few cases which are below 0.1. Due to the fact that I do not have replicate, should I consider padj or I can only apply a cutoff (e.g. <0.05) for pvalue?
It would be great if you can guide me