I love that Deseq2 has altHypothesis="lessAbs" !!!!!!! I've used it a ton for RNA-seq. However, now I'm working with mass spect data using limma. Is there a way to make limma do the same thing?
There is no direct support for this by best knowledge. Similar questions have been asked previously in the Bioconductor support forum, for example:
They discuss options around the TOST concept.
From these posts please go back and forth to find other posts in that forum to capture what the developers of limma/edgeR responded on the matter.
Depending on your exact purpose it might even be enough to go for genes with large AveExpr and a nominal (not adj) p-value close to one.