Hi all,

I have some question about the lfcshrink function of DESeq2.

When analyzed using the unshrinkage method in DESeq2, the fold change was overcalculated (Log2FC= ~30), so we are trying to apply the shrinkage methods in DESeq2. There are three methods (apeglm, ashe, normal) introduced in the DESeq2 vignette, and among them, I would like to use the "normal" method. This is because fold change is calculated for values within a more general range in the "normal" method. (not close to zero)

But people, including developers (Michael Love), don't seem to recommend the "normal" method. I know that the apeglm method is a better method, but the Log2FC value is almost 0 in the "apeglm" method. I think they're just recommending using "apeglm", not saying you shouldn't use "normal".

1) Is using the "normal" method itself a wrong thing? 2) Is there a way to get more general FC values (values that are not close to 0) while using the "apeglm" method?

Thanks in advance,

Joonhong