I am analyzing the RNA-seq data of cell line. I am comparing two treatment conditions with control and with respect to each other. I found very high Log2 fold change values for differentially expressed genes because of very low values of FPKM in control sample. I have consulted some of papers in which they set the threshold for example, >1 FPKM values for differential expression. How to set this threshold. What is the basic criteria of selecting this threshold value. How the density plots are helpful in this regard. Looking forward for the best possible answers.