flowClean

The software tool 'flowClean' enhances quality control in flow cytometry. This field has seen significant advancements with the integration of high-throughput systems capable of analyzing hundreds of samples per day. Despite these advancements, maintaining data quality remains an important challenge, especially in experiments measuring many parameters. An analysis of 29,228 FCS files from global laboratories revealed that 13.7% exhibited fluorescence anomalies, which can arise due to fluctuations in fluid dynamics affecting the stability of fluorescence measurements over time. These instabilities can vary across samples and parameters, leading to the potential emergence of false cell populations in the data.

To address these issues, 'flowClean' employs an innovative algorithm that monitors changes in subset frequency within a sample across the acquisition period, using the centered log-ratio space for tracking cell populations. This method allows for identifying and flagging time periods where fluorescence perturbations occur, thereby highlighting potentially aberrant data. These flagged events are added as a new parameter to a revised data file, enabling users to identify and exclude these periods from further analysis quickly.