Hello, I have a small dataset with 3 replicates per condition. One condition is a gene over-expression, the other is a control. I'm used to run DESeq2 with betaPrior = True to have a comparability with the 'old' DESeq2 behavior. I can't apply this old workflow because the expression differences between my conditions it quite small and one gene, namely the over-expressed ![](https://ibb.…

better just use non-shrunken log2foldchange for all? (I'm looking forward to `` apeglm ```` ``and `` ashr ``) Thank you

setwd("C:/cygwin64/home/Coexpression_Nov2017") getwd() library(DESeq2) library(apeglm) library(ashr) expected_matrix <- read.table(file = "17samples_expected_count.txt", sep = "\t", header = TRUE) condition <- factor(c (rep("control