Compensation

[PhillipSsekamatte]

Dear Helena, How would you perform compensation of flow cytometry datasets using CATALYST?

[HelenaLC]

You wouldn’t. The package was originally developed for CyTOF data. While most visualizations and analyses are applicable to FACS, the compensation procedure is not, as it relies on single-stained beads for spillover and background signal estimation. I’d suggest looking into the flowCore package instead, which is a long-standing framework for FACS analysis in R.