How the experiment-wide compensation works in Cytobank


When you have selected an experiment compensation matrix in the Compensation Editor on the Cytobank platform, it will be used as an experiment-wide compensation for all other parts of your data analysis including GatesIllustrations, 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  



Advanced analyses 



How to set an experiment-wide compensation   

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


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 impacts 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 Active Compensation. 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.  



If you changed the experiment-wide compensation after creating gates, those gates will be hidden. When you click on the hidden gates, an error message will show up under the Active Compensation showing the name of the compensation that was used to draw the gates. You may either go to the Compensation Editor to change the compensation back or re-draw the gates with the new compensation selected.  


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

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

When importing gates via GatingML into an experiment with no gates, the experiment-wide 

compensation will be set to the most commonly used compensation among gates imported.  

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



The illustration will automatically use the 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 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 run will be blocked. Please refer to the FlowSOM and CITRUS articles for more information.  

You will be able to 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 and the viSNE and SPADE analysis set up. 


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 


Have more questions? Submit a request