Starting with version 10 of FlowJo, there is a new interface for viewing compensation matrices – the Matrix Editor. This page describes the Matrix Editor. The matrix editor window can be …

When fcs3.0 files are loaded into FlowJo, the acquisition matrix is applied automatically using the $SPILL keyword embedded within the file. The acquisition matrix can be modified by double …

There is a single compensation matrix in the workspace by default and it will allow you to create one new compensation matrix in FlowJo. If you require multiple new compensation matrices, …

For version 10, there are three main components to the user interface for Compensation: The Matrix editor – used to view/adjust matrix numbers with a preview of the changes. One other …

This page will help acquaint you with the various ways to interact with Compensation Matrices in FlowJo. For your convenience, this document is broken into chapters.

The file contains the title of the compensation matrix, the names of the parameters/channels used in the matrix and the coefficients of the compensated parameters.

To edit a matrix, select it from the matrix list in the hierarchy, open the compensation editor and click the Edit Matrix button (Figure 2). This will display the selected matrix, and enable editing.

Good compensation matrices are derived from good compensation controls! There are two of different ways in FlowJo vX to alter spillover values in an existing acquisition matrix. The two …

The Compensation Wizard will automatically assign single stain controls to detectors, create clean-up gates, create positive and negative gates if AutoSpill is not used, and identify …

FlowJo computes the compensation matrix on control samples much the way you would manually set the compensation. To do this, you will select gates on positive and negative populations for …