domains / families / science / differential-analysis

differential-analysis

authentic

Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell populations change in frequency or marker expression between conditions using diffcyt (edgeR/voom/GLMM for DA, limma/LMM for DS), with cydar, CITRUS, and compositional methods (sccomp, scCODA, DCATS) as alternatives. Covers the sample-is-the-experimental-unit principle, design/contrast and mixed-model formulas, compositionality of cluster proportions, and FDR across clusters. Use when comparing populations between groups, choosing a DA method, handling paired/batch designs, or deciding whether compositional correction is needed.

When to use

• comparing populations between groups
• choosing a DA method
• handling paired/batch designs
• deciding whether compositional correction is needed
• testing cluster frequencies (DA)
• testing within-cluster marker expression (DS)
• compositional re-check for artifactual depletion

When not to use

• per-cell tests treating cells as independent observations
• DA from a single sample per condition

Skill page

Source