Categorizing files as Experiment Files, Compensation Controls, and Other Controls


In the Cytobank platform, any FCS file included in an experiment must be categorized according to one of three designations that impacts the behavior of the file within the Cytobank experiment: 

  1. Experiment Files
  2. Compensation Controls
  3. Other Controls

Upon upload, the Cytobank platform will attempt to automatically categorize your files into these designations according to the file and sample name. Files containing terms such as beads, comp, FMO, etc., will be categorized into one of the Control designations by default. Most files will end up as Experiment Files. 

The category that each file belongs to can be viewed under Sample tags ->Assign panels. 



(From the panel setup page, click to Configure control files to display the file categorization menu. Files are categorized as Experiment Files, Compensation Controls, and Other Controls. Note that this is a partial list of files for example purposes)  

Details on Each File Category

Each designation has a different effect on the way in which the files appear and are accessed within the Experiment. The salient points are listed below.

Category Effect in Experiment
Experiment Files - Files appear everywhere within the experiment and are fully available for all analysis methods
Compensation Controls

- Files are hidden from most parts of the Experiment, except for workflows on the Compensation page

- Files are unavailable for any analysis methods outside of the Compensation page

- Files don't appear for panel assignment on the panel setup page

Other Controls

- Files are visible and available for analysis within the Gating Editor, Illustration Editor, and Sample tags pages. Usually FMOs and isotype controls are designated as Other Controls

- Files are not visible or available for analysis for SPADE, FlowSOM, viSNE, CITRUS, or Export Statistics (this behavior for exporting statistics can overridden during export setup)


Change the Categorization of Files in an Experiment

To adjust the categorization of any file in the Experiment, first navigate to the Assign panels for an Experiment.Once on the panel setup page, open the file categorization dialog (see image above in background section). 

Click the radio buttons to assign individual samples to categories. Filter the visible files and then use the column buttons to assign categories in bulk.



(Files are moved between Experiment Files, Compensation Controls, and Other Controls categories. Files can be assigned individually or in bulk)

File categorization after PeacoQC run

Once the PeacoQCprocess has run successfully, you would notice that the original compensation files are now categorized as other controls instead of compensation controls. This behavior is to avoid any confusion in case you would like to use QC compensation files to create a new matrix using the automatic compensation tools.


(Original compensation files being placed in Other Control category to separate them from QC’ed compensation files)

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