FCS Express: Compensation

Overview of Compensation in FCS Express


With FCS Express you don't have to throw data away just because it was improperly compensated on the instrument. You can compensate your data directly on your analysis computer. FCS Express allows you to have many compensation sets defined for the same layout. That means that you can have files from different days open in the same layout, and each of them can be using a different set of compensation settings. You can also store your compensation settings directly with the FCS file or in the layout, so that every time you load up your data, the proper compensation will automatically be applied.

Manual Compensation Sliders
Uncompensated Data
Compensated Data

Manual and Automatic Compensation via the Compensations Navigator

FCS Express provides two convenient ways to compensate your data. You can set up the compensation manually, by entering the percentages or using slider bars to subtract for every parameter, or FCS Express can calculate the parameters for you. With the Automatic Compensation Setup you just have to tell FCS Express where your positive and negative populations are in your single stained controls, and it will calculate the appropriate compensation parameters. The compensations navigator (below) will help organize and make sense of your compensation defintions and will color code compensations to highlight high and low values..

The compensations navigator organizes compensations and makes them accessible with one click. Use the navigator for many common commands such as renaming, deleting, adding, and copy and pasting compensations. Color coding will help visualize high and low values.


New drag and drop capabilities allow you to apply any compensation to any plot with one click. You can even drag and drop compensation definitions from one layout to another!

Drag a compensation defintion to a plot (left arrow) and drop it to apply the compensation (down arrow).


Manual compensation can be defined in the compensations navigator or with easy to understand sliders. For more information please the video below, manual compensation section of the manual, or try it out for yourself with the manual compensation tutorial.

Manual Compensation in FCS Express


The Automatic Compensation Setup takes you through the compensation process in a few easy steps. Just select your stained and unstained controls, build histograms, and click calculate matrices. For more information please the video below, the automatic compensation setup section of the manual, or try it out for yourself with the automatic compensation tutorial.



Automatic Compensation in FCS Express