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compensation-transformation

separate

Corrects fluorophore spillover (conventional compensation) or spectral overlap (spectral unmixing) and applies variance-stabilizing transforms (logicle/biexponential, arcsinh, log) for flow and mass cytometry. Covers spillover-matrix estimation from single-stain controls, AutoSpill, the spillover spreading matrix and why panel design (not compensation) bounds resolution, compensate-then-transform ordering, and arcsinh cofactor choice (5 for CyTOF, ~150 for fluorescence, per-channel via flowVS). Use when correcting spectral overlap, preparing data for gating/clustering, choosing logicle vs arcsinh, deciding a cofactor, or distinguishing compensation from spectral unmixing.

When to use

• correcting spectral overlap
• preparing data for gating/clustering
• choosing logicle vs arcsinh
• deciding a cofactor
• distinguishing compensation from spectral unmixing
• spillover-matrix estimation from single-stain controls
• AutoSpill
• spillover spreading matrix

When not to use

• fixing smeared negative populations by tuning the matrix
• over-compensating to flatten variance

Skill page

Source