I have pretty simple but probably weird question. I have complex design with interaction terms in my model (see below), I run DESeq2_1.20.0 on rna-seq data. It seems that I can't change my contrasts to end up using only apeglm shrinkage and lfcThreshold, instead I'm stuck with using ashr shrinkage method without being able to incorporate lfcThreshold into calculation of null.
What bothers me is that all published papers are using simple comparisons, at least in plant science, but all, test against non-zero log fold change. If me using ashr shrinkage and definitely avoiding doing any post-hoc on lfc, how can I justify not incorporating lfcThreshold?
previously suggested by Michael L. model matrix for my study.
mm <- model.matrix(~cltv + cltv:time + cond:cltv:time, data=colData(dds))