Can I use the FlowClean R Script with FCS Express?

Yes, with FCS Express 6 or later, you can run the FlowClean R Script via the R Integration.

About FlowClean

FlowClean is an algorithm and tool for quality control, designed to identify fluorescence abnormalities caused by fluidic issues at the time of acquisition. FlowClean tracks subset frequency changes within a sample during acquisition, and "flags" time periods with fluorescence perturbations that could possibly lead to the emergence of false populations. The result of the FlowClean R script, when used in FCS Express, is a new parameter, called FCSE_GoodVsBad. The end user can utilize the newly-created parameter to exclude events within aberrant time periods.

The FlowClean algorithm can be run from within the R Integration tool of FCS Express 6 or later by using an adapted version of the original (flowClean_1.12.0) code. For simplicity, the original script has been adapted to use a matrix as input parameter instead of a standard FCS file, while the remaining portions of the code and algorithm are unchanged.

Note: the original FlowClean script works on raw fluorescence data, which are uncompensated and not transformed (i.e. linear) for FCS 3.0 and 3.1 files. However, the matrix exported by FCS Express into R reflects what is displayed in the plot to which the transformation has been applied. Since compensated data are usually displayed in the plots, these compensated data will be exported to R instead of uncompensated data. The results obtained when FlowClean is run through FCS Express will not reflect the results obtained when FlowClean is run directly through R. The same consideration needs to be taken into account with regards to parameter scaling. By default, FCS Express exports fluorescence parameters with biexponential scaling. When this is the case, the results obtained when FlowClean is run through FCS Express may not reflect the results obtained when FlowClean is run directly through R. The scale applied to parameters when exported to R can be customized (e.g. set to linear) in the Transformations dialog.

For more details about the modifications made to the original script in order to be run through FCS Express, please see the comments within the script or contact us at

Please Note: The FlowClean R implementation may fail on a wide variety of data files due to the algorithm itself failing. Please use this tool at your own risk. 

How to Use the FlowClean R Script

FlowClean makes use of additional R packages that must be installed via R prior to using in FCS Express.
  • To install the FlowClean package, please run the following lines in your R console:


  • To confirm the installation was performed properly, please load the FlowClean package in your R console by running the following line:


  • The following lines should be returned, which verifies the package was installed properly:

> library("flowClean")
Loading required package: flowCore

If any errors or problems are encountered, please contact us at

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