We have been applying lfcThreshold test in DESeq2 with altHypotesis=lessAbs to find what microRNAare significantly stably expressed between matched fresh frozen and formalin-fixated paraffin-embedded tissue. In the official manual, they use lfcThreshold=0.5. When we use the same threshold, we don't get any significantly stable miRNAs using the BH-adjusted p-value (and just a few for non-adjusted p-value). We have also tried with lfcThreshold=0.75 and lfcThreshold=1 with obviously better results.
My question is: What can be considered a good lfcThreshold-value for finding stably expressed microRNAs?
As far as I can see the significance is calculated from baseMean and it's standard error.