FCS metadata is not just the filename
The FCS format stores event data together with keyword information, such as channel names, acquisition details and, when provided, sample or plate identifiers. A filename is a separate label chosen by the exporter or researcher.
Optional fields are not guaranteed to be present. A recorded tube name does not establish a treatment, donor or biological replicate. Those experimental labels may need an external sample sheet.
Choose the source for the field you need
| Source | Useful for | Check first |
|---|---|---|
| FCS keywords | Recorded acquisition and sample information | The original key and actual value, not a guessed meaning. |
| CSV sample sheet | Researcher-confirmed treatment, donor, timepoint and other labels | One matching sample identifier per row and non-conflicting field names. |
| Filename blocks | Labels encoded in a consistent naming scheme | The chosen delimiter and the preview for every file. |
These sources can supplement different fields in one metadata table. They are not three competing grouping modes. Prefer a documented source for each field rather than conflicting labels.
In FlowApp: maintain fields first
- Open metadata editing from the project/workflow controls, or Manage metadata while creating a sample group.
- Click a field to inspect its source and available values. FCS-derived fields are read-only in the field editor; add a new custom field rather than editing the recorded value.
- Use Import CSV alongside Add field for a sample sheet. The sample column should contain the imported filename. CSV columns with existing names can update those fields, so review names and values before import.
- For filename labels, add or select an editable field and choose Extract from filename. Select the relevant text blocks on a representative name; one field may combine several blocks.
- Review the preview across files before applying. Inconsistent delimiters, missing blocks or ambiguous labels require correction, not an inferred meaning.
A filename example
Blood_Control_Day7_Donor01.fcs
This is an invented naming example. You might explicitly map Blood to specimen, Control to condition, Day7 to timepoint and Donor01 to donor. The mapping is your experimental convention, not evidence that a string carries that biological meaning.
For filenames that encode several attributes together, use separate fields where you intend to compare separate dimensions. An opaque combined label is less useful than explicit condition, timepoint and donor columns.
Create groups only after checking metadata
In Groups, create a new sample group, choose metadata matching, select the field and the desired values, and review the member files. Metadata editing does not automatically create GRPs.
For a cross-group report, avoid selecting overlapping groups as if they were independent. A donor ID identifies an experimental unit only if that is appropriate to the design; it is not the same thing as a filename or tube ID.
Before a report
- Check missing values and accidental spelling variants such as Control and Ctrl.
- Verify how many actual samples each selected value includes.
- Keep technical repeats distinct from biological units, and use an explicit ID for pairing.
- Do not publish personal identifiers in exported reports or optional AI requests.
Reference and next steps
The FCS 3.1 standard paper describes standardized metadata and optional sample/plate identifiers. The editing and grouping steps above describe FlowApp.