In order to compensate a file, FlowJo needs to create new parameters to contain the compensated data. Thus, compensated files take up more memory than uncompensated files. To figure out how much memory you will need to allot FlowJo, see the page on memory requirements.

To change the amount memory, you will need to quit FlowJo. Select the application file in the finder (click on the application once you have opened the folder where FlowJo is kept), and select "Get Info" from the Finder's File menu. In the box labeled "Preferred Size", enter the amount of memory that you have calculated above (or a greater amount). Then you can restart FlowJo.

If you cannot launch FlowJo with the amount of memory necessary, you have only three options: (1) buy more RAM; (2) turn on virtual memory; (3) go to a machine with more memory.