1. Choose the report objects
| Report scope | Included objects | A useful starting point |
|---|---|---|
| Sample report | Selected samples, their population statistics and plots | Inspect a sample's gating strategy and measurements. |
| Within-group report | Samples in one selected group, with optional group-level plots and summaries | Review consistency and sample variation within that group. |
| Cross-group report | Selected groups, their summaries and optional individual-sample details | Compare groups while retaining the observations behind the summary. |
Group membership does not establish independence. Several tubes from the same donor may represent repeated or technical measurements. An overlay made by pooling events is a distribution view, not a set of independent replicates.
2. Configure charts and statistics
In the report builder, choose quick or advanced settings. Advanced mode lets you add, remove and reorder chart configurations, each with its own population, metric and title. Save your choices as personal defaults in the current browser; they are not a mandatory template.
- Choose %Parent, %Total, event count, mean fluorescence intensity or median intensity. Specify the channel for intensity statistics.
- Use individual dots to retain sample values. Box, violin, mean/error-bar, paired, trend and heatmap views are available, subject to the data each requires.
- For paired measurements, specify the experimental-unit field; files are not paired by row order.
- Describe error bars as SD, SEM or confidence intervals. These answer different questions.
Descriptive statistics are the default. Supported tests include Welch and paired t-tests, Mann-Whitney U, Wilcoxon signed-rank, one-way ANOVA, Kruskal-Wallis and Friedman, with the application's data and design checks. Choosing a test does not verify its assumptions. Some results are withheld when units, pairs or sample sizes are insufficient.
This release does not provide multifactor or mixed-effects models or post-hoc tests after an omnibus comparison. Trend lines connect observed summaries; they are not fitted statistical models. See the statistic definitions before choosing outputs.
3. Arrange, annotate and export
Set figures per row with a numeric input; the default is two. In preview, change the count again, reorder figures within their chart section, and set a figure's column span. Narrow screens reflow to one column.
Use the preview editor to revise text and add sections, or place rectangles, ellipses, arrows and text on figures. Annotations do not change gates, measured values or calculated statistics.
| Output | What can be changed afterwards? |
|---|---|
| HTML | The exported file includes an offline editor. Change layout, text and annotations, then save a revised HTML. |
| Static pages retain the chosen layout and annotations. Edit the HTML/source, then export PDF again. | |
| PowerPoint | Review the exported slides in your presentation software. Figure annotations are composited into the images. |
Figure reordering is within a section, not an unrestricted whole-page canvas. Saving standalone HTML creates a revised file through the browser; it does not silently overwrite the original.
4. Try a complete synthetic example
Open the editable example report or start with the same built-in demo cohort.
- Open the three files named Demo cohort 1.fcs, Demo cohort 2.fcs and Demo cohort 3.fcs.
- Create one group containing file 1, called Control, and another containing files 2 and 3, called Treated. These labels are invented for demonstration.
- On FSC-A / SSC-A, define the illustrative cells rectangle shown in the table below. Under it, define the illustrative CD3+ rectangle, and apply the hierarchy to both groups.
- Choose a cross-group report and advanced settings. Keep descriptive-only statistics, add individual dots, a mean/SD chart and a heatmap, then generate.
- In the exported example, change figures per row, annotate a figure and save HTML. Reopen it to check the revision.
| Gate / parent | X channel and raw bounds | Y channel and raw bounds |
|---|---|---|
| Illustrative cells / All Events | FSC-A: 35,000 to 150,000 | SSC-A: 8,000 to 90,000 |
| Illustrative CD3+ / Illustrative cells | CD3 FITC: 12,000 to 262,144 | SSC-A: 8,000 to 262,144 |
All three files are synthetic software examples. The invented group sizes are n=1 and n=2. No p-values are reported and no biological response can be inferred. The coordinates are not an assay protocol.
5. Check the finished report
- Verify sample identities, group membership, parent populations and percentage denominators.
- Record compensation, transformations and QC status, including QC not run.
- Check the experimental unit, valid counts, missing values and statistical limitations.
- Review figures and labels in the exported file, not only in preview.
Finished reports and personal defaults are browser-local, not a cloud backup. UI navigation can leave generation running in the background; closing or refreshing the page can interrupt unfinished work. Optional AI summaries require a configured provider and researcher review.
Related resources
Metadata and groups · Gating hierarchy · QC flags and review · Compensation checks · Report history and data handling