I got a couple questions this week about combination gates, so here is a short explanation of how they work.

Combination gates in FlowJo use a small number of user defined gates (n) to identify a relatively large number (2^n) of potential populations in your FCS file.

Here is one way of thinking about this:

1) FlowJo looks at the gates you drew, and adds an invisible inverse of each gate ( a "not" gate). This is indicated in FlowJo through a plus sign for a normal gates, and a minus sign for not gates.

2) FlowJo then applies a factorial method to identify all of the possible combinations of the new (2n) set of gates. This is similar in concept to a factorial experiment.

3) Each of the newly derived combinations (2^n) is then listed in the workspace as a single gate saving you the trouble of having to identify all of these combinations hierarchically - a major pain for any more than two initial gates.

A fun way to visualize this is to think about hypercubes. Figure 1 correlates a two initial gates to a 2-cube, and Figure 2 ties 3 initial gates to a 3-cube drawing, both done in keynote. Bonus points to anyone that can extend this to 4 initial gates using examples of the 4-cube shown in the wiki article linked above.

(Click on images to view full size)

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