Flow Summary
Population frequencies, MFI summaries, and group comparisons from flow cytometry exports
Once you've gated your flow data, you're left with a table of population frequencies and signal intensities. This workflow takes that export, summarizes it cleanly, and runs the statistics comparing populations across your conditions.
What it measures
- Population frequencies. Percent of parent (or of a fixed reference population) for each gated subset.
- Expression. Median or mean fluorescence intensity (MFI) per marker, summarized across samples.
- Group differences. How those frequencies and MFIs shift between treatment, genotype, or timepoint.
Data you upload
- A summary table exported from your gating software - one row per sample, columns for each population's frequency and/or MFI.
- A grouping column (condition, donor, timepoint) for the comparison.
This guide covers the summary-table workflow. For raw FCS ingest, interactive gating, compensation, and FlowJo workspace import, use the Flow Cytometry Workspace.
What you get back
- Per-population summary statistics (mean/median, SD, range) for each group.
- Comparison plots with significance annotations across conditions.
- An MFI summary per marker where intensity values are provided.
Method note
Frequencies are bounded proportions, so the agent checks whether a variance-stabilizing handling is warranted before comparing them, and falls back to a non-parametric test when group sizes are small or normality fails. The comparison itself reuses the Group Comparison engine, including effect sizes and multiple-comparison correction across a panel of populations.
Related
For spot-based immune readouts, see ELISpot. For soluble-analyte panels, see Multiplex Panels. For the comparison statistics themselves, see Group Comparison.