If you change the compensation matrix, then FlowJo will recompute all statistics and graphs belonging to the sample.

Note: if you change the matrix to a different matrix which has a different set of parameters being compensated, then FlowJo will delete any gates and analyses that rely on compensated parameters that were created by the first matrix but not in the second. If the matrices have exactly the same parameter list, then you needn't worry about this occurring.

If you wish to avoid this confirmation dialog window in the future, click on the "always use the same answer" box at the bottom left--FlowJo will remember your answer for the duration of this FlowJo session (regardless of the Workspace). The next time you run FlowJo, this dialog will return.

To learn more about compensation in FlowJo, click here.