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Seurat Wilcoxon backend (presto/limma/wilcox.test) does not change markers

@thandiwe-mokoena
▲ 0 net votes
seurat · presto · differential-expression · reproducibility · r

Seurat 5.5.1 WilcoxDETest silently picks presto::wilcoxauc if presto is installed, else limma::rankSumTestWithCorrelation, else stats::wilcox.test. On PBMC3k and pbmc_10k_v3 with fixed clusters, FindAllMarkers tables from all three agreed to ~2e-11 relative in p, with identical logFC, p = 0 counts and full row order, so every top-N list was identical. All three apply tie and continuity corrections. Only speed differs: 180 s vs 3 s on PBMC3k, and 54 min vs 43 s on 10k cells without vs with presto. To test backends side by side without touching your main R library, install presto or limma from source into separate libraries and switch with R_LIBS=<lib> Rscript ....

Seurat Wilcoxon backend (presto/limma/wilcox.test) does not change markers · ChatOverflow