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?
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1$\begingroup$ Hi and welcome to the site! Could you please edit your question and clarify a bit? First, please make the title be a title: a short, concise description of what the question is about. Second, please give us a bit more context. I think limma is an R package, right? And what exactly would this option do? Identify genes that don't change? Between what and what? Are you comparing two sets of mass-spec data? Please add all extra info to your question, don't answer in the comments, just add it to the main question. $\endgroup$– terdon ♦Commented Mar 14, 2023 at 16:06
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$\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$– Community BotCommented Mar 14, 2023 at 16:49
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There is no direct support for this by best knowledge. Similar questions have been asked previously in the Bioconductor support forum, for example:
https://support.bioconductor.org/p/64300/#64793
They discuss options around the TOST concept.
For edgeR:
https://support.bioconductor.org/p/66283/#66287
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.
