Create Comp Matrix allows you to make a compensation matrix in OMIQ, from single stained (single color) controls and apply it to your files. If you prefer to learn by watching, then click here to go to the Compensation section of our tutorial.
Looking for how to create and apply a Spectral Unmixing Matrix? Find that here.
1. Add a Scaling Task off the Workflow Root task

Click Add new child task on the Workflow Root task and select Scaling from the task selector. Adjust your Scaling settings - find out how to scale your data in OMIQ here.
By default, new Workflows go from Workflow Root → Compensation → Scaling... However, you must scale your single color controls prior to performing Create Comp Matrix. Therefore, you must make a second branch of your Workflow, as described above.
2. Add Create Comp Matrix Task

Click Add new child task on the Scaling task created in Step (1) and select Create Comp Matrix from the task selector.
3. Choose your Channels

Click Choose Channels, select the channels for which you have single color controls for, then click Submit.
4. Configure your Positive and Negative Controls (if necessary)

OMIQ attempts to select these automatically. Click Configure +/- Controls to review the configuration, then click Submit.
If you are using unstained cells as your Negative control, you can enter that in on one row, and then copy to all other rows by clicking on the ⫶ → Apply value in col2 to all.
5. Generate and Activate Clean Up Gates

On the flow cytometry plot, select the File you want to make any clean up gates on and choose the relevant XY axes. In this example we are using compensation beads so have selected the first File that contains compensation beads and changed the XY axes. Create your clean up gate → Activate the gate → Click Generate Gates.
Note that you can include clean up gates from multiple files and filters. For example, if you wanted to use a mix of control samples that were cells or compensation beads. To do this, perform the step above on the different Files. Activate one of the clean up gates → Click Generate Gates → Right click on the Compensation Gate you want to move → Copy Node → Paste Node on relevant Clean Up Gate.
6. Review Compensation Gates

Optionally you can click through your gates and make any necessary adjustments.
7. Generate and Copy Compensation Matrix

Click Generate Comp Matrix (you may need to scroll down to see this step) → Copy Matrix.
The Comp Matrix you have created is not automatically applied to your data. To apply this Comp Matrix to your data, follow the instructions in Step (8) below. Additionally, note that if you exit the Create Comp Matrix task, and enter it again, the Comp Matrix is not automatically shown. Click the Generate Comp Matrix button again to regenerate your Comp Matrix.
8. Copy and Apply Compensation Matrix

Save the Create Comp Matrix task → go back to your Workflow → Open the Compensation task that is there by default, in the first Workflow branch → click ⫶ Actions → Paste. Your compensation matrix will now be applied to the files indicated in Files in Group. Save the Compensation task → go back to your Workflow and continue with the downstream tasks.
You can view NxN plots easily in Figure, find out how here.