In this post, Mike Love explained the reasoning for moving LFC shrinkage into its own step using the
lfcShrink function, decoupling testing from shrinkage.
Is there any way to use
apeglm-shrinked LFC to compute p-values (similar to using
betaPrior=TRUE, but with the new estimator)?
I know that you can get significance levels when you use
apeglm. Is there a reason that this is only possible when you incorporate
lfcThreshold into the null hypothesis?