Warnings on FCS files: Understanding the Cytobank File QC system

Cytobank is committed to supporting standards in the flow cytometry community. Towards this goal, we have implemented a file quality control system, where we provide more information to customers about how your files support the standard specifications set forth by the International Society for Advancement of Cytometry (ISAC).

In cases where files do not match up to the specifications, we present the following indicators next to the FCS file names on the Experiment Summary page:


red error icon - The file is missing information required for analysis, or is missing information that is deemed mandatory by ISAC. In most cases we recommend that you do not use this file, as the missing parts could indicate missing data or data that could be parsed incorrectly. Examples include: truncated data where the header and data segment do not match, or the header is missing required parameters essential for parsing and interpretation of the file.


info icon - The file is not up to the specifications outlined by ISAC; however, this likely does not affect your data analysis.


How to move forward

Sometimes, even though your files are not written according to ISAC standards, Cytobank can still correctly parse your data. This can be the case when you are missing the $BEGINDATA and $ENDDATA keywords. To see if things are okay, navigate to the gating page and view your data. If it seems acceptable, then Cytobank is likely parsing your data correctly. To get rid of the File QC warning, rewrite your files within Cytobank.

If you have a different File QC message regarding a truncation or other problems, you can try reuploading your data to Cytobank. If the problem persists, then your file is corrupted and needs to be fixed. Try redoing any processing steps that happened before upload to Cytobank, or contact the creator of the software that produced your FCS files.

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