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To manually enter a gate, display the graph on which you wish to enter a gate. (For instance, to manually type in a lymphocyte gate, you might display Forward vs. side scatter). If you display a histogram or CDF, then you will be entering a one-dimensional gate. From the "Graph" menu, select "Manually enter gate". You will be presented with the following dialog:
Note that you can enter the gate in units of channels, absolute intensity, or percentile. FlowJo tells you the minimum and maximum acceptable values for the gate. When you select "percentile", then FlowJo creates a gate based on the percentiles that you enter. For instance, if you select a gate that has a lower bounds of 50 and upper of 100 (for percentile), then FlowJo constructs a gate which includes the brightest half of all of the events. Likewise, a percentile gate of 0 to 5 results in a gate for the dimmest five percent of the events. When you make a new gate based on the fluorescence distribution (percentile), the gate is stored in terms of the channel numbers. Thus, when you copy the gate to another sample, it is copied with regard to its position in the window. This way you can make a gate on the brightest 5% of events, copy it to other samples and see what fraction of events are above that value in those samples. |
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