I believe we use the same formula as FlowJo. The results we get are nearly identical, and the formula is very simple.
The spill value for FL-1 into FL-2, for instance, is the difference, for the FL-1 compensation control, between the median FL-2 fluorescence values of the positive and negative populations, divided by the difference between the median FL-1 fluorescence values of the positive and negative populations.
When you are using LabKey to calculate the compensation matrix for multiple runs, we recommend that you use gates which are smaller than you would use if you were drawing the gates by hand for each run. This is because there will be variation between the runs, and you want to make sure that the indeterminate cells in the middle are not used in the calculation.
In practice, it does not make much difference whether these cells in the middle are included in the positive or negative populations. The only values that matter in the calculation are the median fluorescence values, and including these small numbers of cells does not change the median by very much. |