Compensation Interface

The graphic below shows the Define Matrix tab and its controls. There are several ways to apply the positive and negative populations you have defined into the comp matrix dialog boxes.

The most direct is to define a positive and negative population on each single stained comp control sample and drag each of these to the boxes beside the appropriate parameter. Boxes at the right show a petri dish icon to indicate that they contain a control sample.

a) Drag the positive and negative subsets from the workspace to the boxes beside each parameter in the Comp Definitions window.

OR

b) Drag a subset that has one or two gated subsets to the AutoAssign Box. FlowJo looks at each subset you drop on it, and looks for child gates. If there is only one child gate, it assumes that this represents a positive comp control population. If there are two child gates, it assumes that there is a positive and a negative. You can Control-select several parent populations and drop them on AutoAssign at once.

OR

c)You can have a universal negative that can be used for all compensation controls that have only positive populations. For example, when using antibody capture beads to compensate, each sample has beads that capture one color (with no negatives). Another sample contains unstained beads and is used as the negative population for each parameter. Drag an unstained sample or negative subset to the Universal Negative button. FlowJo puts this negative population into all the negative boxes for each parameter. In general, you should drop the universal negative on the comp window first--because if you do it second, it will replace any existing negative populations you have already added.

If you have dragged the incorrect population into one of the boxes, simply click it and hit the Clear button that pops up, to remove it from the box. Or, you can drag and drop the correct population onto the box, replacing the existing one. You can know what population is in a box by hovering over the box with your mouse. The name of the population that you dragged into the box will be displayed.

Note that some flow cytometers collect a fluorescence parameter in the SSC-W channel. This channel will therefore be displayed in the compensation dialog window when sample files in the workspace contain this parameter.

Likewise, DiVa data will show its accompanying compensation matrix when you first open the compensation window.

Go back to the overview of compensation.