In DESeq2, it's possible to keep the unshrunk fold changes in
results() output using
addMLE=TRUE, but that requires
betaPrior=TRUE. This behavior seems to be based on the old workflow.
The more modern approach is to use
lfcShrink(), but then the unshrunk fold changes are lost. Is there a way to run
lfcShrink(), but somehow retain both types of fold changes? It's possible to take the fold change before and after
lfcShrink(), but that seems not optimal.