Most approaches to testing for differential expression, including the default approach of DESeq2, test against the null hypothesis of zero LFC. However, if any biological processes are genuinely affected by the difference in experimental treatment, this null hypothesis implies that the gene under consideration is perfectly decoupled from these processes. Due to the high interconnectedness of cells’ regulatory networks, this hypothesis is, in fact, implausible, and arguably wrong for many if not most genes. Consequently, with sufficient sample size, even genes with a very small but non-zero LFC will eventually be detected as differentially expressed. A change should therefore be of sufficient magnitude to be considered biologically significant. For small-scale experiments, statistical significance is often a much stricter requirement than biological significance, thereby relieving the researcher from the need to decide on a threshold for biological significance.
