...
Please remember we recommend compensation controls to be made and acquired in a similar manner and in parallel with your samples. We also recommend running and recording calibration beads both before and after your acquisitions to not only show the instrument was stable throughout the acquisition but to provide target MFIs in the event that application settings cannot be used on subsequent days.
...
Understanding negative fluorescence values and baseline restore
You may find yourself thinking it odd to have negative fluorescence values being reported in flow data files when the absence of fluorescence on a particle, one may think, should equate to either a zero or a low positive value. This can however occur because the values reported are arbitrary measurements of fluorescence on cells due to digitization.
...