How the experiment-wide compensation works in the Cytobank platform


When you select a compensation matrix in the Compensation Editor on the Cytobank platform, it will be used as an experiment-wide compensation for all your downstream data analysis, including Gates, Illustrations, and the Advanced analyses.  

In this article, we will discuss how the experiment-wide compensation behaves with each analysis part, and how to change it.   

How to set an experiment-wide compensation

How the experiment-wide compensation behaves within different parts of the analysis    

1) Gates

2) Illustration

3) Advanced analyses

4) Others

How to set an experiment-wide compensation    

Access the Compensation page by clicking the Compensation tab at the top right corner on the experiment level navigation bar. If the navigation bar doesn’t contain Compensation, please click Actions -> Edit Compensation to access the Compensation page.   


You can examine the current compensation by clicking the drop-down menu next to Experiment compensation under the blue ribbon. Select the matrix you would like to use from the Compensation Editor to be the experiment-wide compensation. If the compensation option you’d like to select isn’t present, generate a new compensation matrix first.



The impact of changing the experiment-wide compensation on the analysis can be found here on How to modify a File-Internal Compensation matrix 

Also, check out all articles on compensation

How the experiment-wide compensation behaves within different parts of the analysis 


 If you have set the experiment-wide compensation prior to gating, it will be the default selected compensation under the Compensation on the top right of the screen. If you need to change the experiment-wide compensation for gating, within the Gating Editor, click on the edit pen from the left pane to go to the Compensation Editor to change the experiment-wide compensation matrix there.  


This would lead you to the Compensation editor page, where you can choose the compensation of your choice.




You will be notified with a message that Experiment compensation was successfully changed.



When importing gates from another experiment, the current experiment-wide compensation will apply to these new imported gates. If the imported gates were drawn with compensation other than the experiment-wide compensation in the experiment, the imported gates will be hidden.  

When importing gates via Gating-ML into an experiment with existing gates, the current experiment-wide compensation will apply to the new imported gates.   

When importing gates via Gating-ML into an experiment with no gates, the experiment-wide compensation will be set to the commonly used compensation among gates imported.   

Experiment-wide compensation will also be applied to the cluster gates.   



The illustration will automatically use experiment-wide compensation. Illustrations created before a change to the experiment-wide compensation has been set or modified will retain their original compensation. In this case, if the illustration has compensation set differently from the experiment-wide compensation, a warning message appears to the left of the navigation bar.   



You can click on the warning sign which will open the More plot settings window shown below. The compensation setting can also be accessed directly from Plots > More plot settings in the Compensation section at the bottom of the window.  



By clicking the red warning, users can decide whether or not to apply the updated experiment-wide compensation settings to the existing illustrations, created with the old setting. By default, the previously saved illustration will keep the old compensation, unless users explicitly choose to match the new experiment-wide compensation. All new illustrations made after the experiment-wide change compensation will use the current experiment-wide compensation setting.   

When importing an illustration from another experiment, it will try to match the compensation by name. If there is no matching compensation in the destination experiment, it will default to the experiment-wide compensation of the target experiment receiving the import.    


Advanced analyses  

The experiment-wide compensation will be the default compensation selection for all advanced analysis algorithms. 



 If you have changed your experiment-wide compensation after making your gates and populations, recheck the gates to make sure they match the experiment-wide compensation; otherwise, FlowSOM and CITRUS runs will not be able to run. Please refer to the FlowSOM and CITRUS articles for more information.  

You can change the selected compensation to a different compensation on the SPADE and viSNE setup pages directly.  However, it is still important to make sure that the same compensation is used for the populations gating and the viSNE and SPADE analysis setup. 


The experiment-wide compensation will be the default compensation selection when performing these tasks: 

Export stats 

Export events 

Scales editor 

Experiment Manager: Expanded Detail View 


 *For Research Use Only. Not for use in diagnostic procedures. 

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