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lmFit + treat + topTreat(sort.by=“none”) for a log-expression matrix.
Clean-room reimplementation of limma’s threshold-relative moderated t-test: McCarthy & Smyth (2009), Bioinformatics 25(6):765-771, doi:10.1093/bioinformatics/btp053; variance moderation from Smyth (2004), doi:10.2202/1544-6115.1027. No limma (GPL) source was consulted; the method follows the published papers and is validated black-box against the binary.