I have just read the vignette about DESeq2 and I have a question about shrunken log fold changes and threshold test.
I use DESeq() and results() functions to get the gene set with absolute LFC > 1. I understood that the tests give me the results with LFC estimated by MLE.
However, some absolute LFC become lower than 1 after being shrunk by lfcShrunk function.
Is it possible and does it make sense testing for statistical significance of absolute LFC > 1 estimated by MAP (apeglm) ?
I apologize if the question has been asked before.
Thanks in advance,