FlowJo v9 Manual


Cells Squished Against the Axis

Cells on the axis

There are a large number of cells squished against one or both axes. This is not necessarily incorrect, as properly compensated data sometimes has a large number of cells against the axis. Click here for more information on why the occurs and how to know if your data is correctly compensated. If you have compensated using FlowJo, the data will be properly compensated. If you compensate when aquiring on the flow cytometer, the data may be overcompensated with too many cells squished against the axis (unless you were careful to make sure that the medians of the positive and negative populations are the same).

This warning was implemented for two reasons.

1) When you have overcompensated your data, too many cells are squished against the axis.

2) When drawing gates to define populations of cells that are negative for one or both of the parameters (i.e., the double negatives or the single positives on a bivariate plot), make sure you include the cells on the axis in your gate. Because a large number of cells may be on the axis, you must draw the gate on the axis to include all the cells in that population.

You can make changes to the warning under the Graphs and Gates tab in the Preferences. To turn the warning off, set the percentage boxes (right) to 100%.

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