Many users choose to calculate a compensation matrix directly on the flow cytometer prior to collecting samples. However, sometimes it becomes apparent during analysis this computed matrix needs adjustment. To modify file-internal compensation, you first need to extract the matrix. On the Illustration page, enter the Compensation page by clicking the "Edit" button next to the Compensation heading under Plot Controls on the left side of the screen. Then click the "Import Compensation" link on the left. Under "Import File Compensation," select a representative FCS file that contains the file-internal compensation matrix and click "Get Compensation." The file-internal compensation matrix values will apear. To make edits, first enter a name and save the matrix. Then you will be able to click inside any cell with a number and edit that numerical value. Changes will be automatically saved. This matrix will now appear under the list of compensation files that you can select from the Illustration Page and from within the Gating applet.

View a short video tutorial on modifying file-internal compensation or modifying a saved compensation matrix.