I have a control vs treated time course RNA-seq plant data for which I am trying to construct gene coexpression network.I have used DESeq2 package to identify differential expression of genes.
My aim is to identify genes that are exclusively differentially expressed in the time course experiment.
What is the safe FDR and fold change values to consider in a RNA-seq experiment ?
Is filtering the DEGs using FDR cutoff >0.05 is alone sufficient to get significant DEGs?
In FDR and fold change, which one should be given the priority for selecting the DEGs ? or should one consider both in order to filter significant DEGs.