Hi, I have been using Flowjo to analyze my flow data. When I plot Fsc vs ssc, it turns out most of the cell events are on the edges? Is there I can do to fix it to make all the events in frame?
Hi Rui,
I should say that I am not an expert in FACS (yet!), but I had the same problem with most of the events being on the edges of charts in FlowJo. What you have to do (in my opinion) is try to adjust settings while you are acquaring your sample in order to put all/most of your events on chart: increase FSC threshold and adjust the voltages. It will move your events on chart. Hope that helps!
If you have the opportunity to run the experiment again increasing the voltages to avoid the events close to the edges, do it!!!
If not, try some features in FlowJoX like adjusting scales with the option "Customize axis" found in a box with a "T" above of SSC box and/or in a box in the right part of the FSC box.
You can find more information at:
http://docs.flowjo.com/vx/graphs-and-gating/gw-transform-overview/gw-tbutton/
This is a quite old question but I have one comment to add to the other answers. Overcompensation will cause the cell events underneath the bottom edge of the axis of that overcompensated channel. That can be recovered by correcting the compensation parameters.
Try to use biexponential transformation in FlowJo / Diva
Biexponential transformation is helpful. But sometimes you still see the events at the bottom of biexponential axis. For example, if AF700 were overcompensated with PE, when I look at PE vs. BV605, I see events of PE channel beneath the axis. I can properly display these events by correcting the compensation. Please check the example plots.
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