Hello Biostars, I did differential expression analysis by DESeq2 whit LFC=1 and FDR=005, but I found a list of significant differentially expressed genes which is imbalanced, (1345 upregulated and 38 downregulated genes). Does it mean my analysis is not correct or this can happen? thanks
When you apply cutoff on basis of p-values, you will get more number of significantly upregulated or downregulated genes. But if you filter those genes with FDR values (<0.05 in most case) the number will decrease. The genes which have FDR < 0.05 are confidently significant. So, if you got less number of downregulated genes, that doesn't mean your analysis goes wrong. It can happen, depending on the controls you have taken.
Then also, I would suggest you to revise LFC cutoff and check your control group is good enough.