Many users choose to calculate a compensation matrix directly on the flow cytometer prior to collecting samples. This matrix is written into the exported FCS files (File-Internal Compensation). However, sometimes it becomes apparent during analysis this computed matrix needs adjustment. To modify File-Internal Compensation, you first need to extract the matrix.
How to access the Compensation Editor
When you navigate to an existing Cytobank experiment, access the Compensation Editor by clicking the Compensation tab on the experiment level navigation bar. If the current setting is Uncompensated, the Compensation button will not appear in the navigation bar. In this case, please click Actions -> Edit compensation to access the Compensation Editor.
(Navigate to the compensation page within an Experiment)
Click the Import button on the page specific navigation bar.
(choose to import a comp from the compensation page)
Under the File-Internal Compensation tab, select a representative FCS file that contains the File-Internal Compensation matrix you wish to use and click Import Compensation. A new compensation matrix will appear on the page, named based on the file from which it was imported.
(Selecting to import a File-Internal matrix from a file)
From the list of compensation matrices, select the one that you extracted from the FCS file. To make edits, click inside any cell in the compensation matrix with a number and edit that numerical value. Changes will be saved automatically and reflected in the plot to the left. Alternatively, you can use the sliders to adjust the matrix values. This will automatically update the value in the matrix table.
(adjusting a compensation matrix manually)
In order to use this compensation matrix, ensure that it is selected as a compensation matrix under the Experiment compensation menu. Please read the next section before making any changes to experiment-wide compensation settings.
All the Cytobank tools automatically use the latest compensation settings after users make a change in the experiment-wide compensation setting page. Please see How the experiment-wide compensation work in Cytobank
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