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2 votes

To find genes that don't change in RNA-seq, Deseq2 has altHypothesis="lessAbs". Is there a way to make limma do the same thing for proteomics?

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 ...
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2 votes

Inconsistent replicate numbers in RNA-seq

It will not do any harm other than a reduction in statistical power compared to more samples per group. Common analysis tools such as DESeq2, edgeR and limma will work on unequal sample size just fine....
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