i have got approx 2500 lncrna and want to find out the differentially expressed genes. i fetched the data for the lncrna from gene_exp.diff. now some of the fpkm values in both control and stress are 0. i have read in a paper that first normalize fpkm values by adding 0.0001 then calculate foldchange and for differentially expressed genes proceed as
upregulated: fold change>=2 and p value <=0.05
downregulated:fold change<=0.5 and p value <=0.05
yet in another paper i read that first filter out fpkm >=0.1 in any tissue.
then after filtering proceed with adding 0.0001 to fpkm and then calculate upregulated and downregulated.
my question: which way to proceed and what is the difference between the two?