SpillComp function and setting threshold and flexrep

[ramay]

Hi,
Thank you for providing this method for CyTOF users! I have used the SpillComp function to test on some fcs files and have a few questions.

1. Can I use compensation after gating cells ? I have already gated cells so was wondering if I have to go back to raw files to calculate compensation and then gate or can I just use this on gated cells. Does this matter?
2. How do the threshold and flexrep variables would affect the compensation calculation? Is flexrep repetitions or the number of components for flexMix?

Thanks in advance for your help!
Hena