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 accessed in two ways:

1) by double-clicking the compensation badge from the workspace window (any compensated sample has this badge next to the sample in the left hand column down the workspace.)

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2) by clicking the “matrix editor” button in the main Compensation window.

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Matrix Editor Window:

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Since this window is complex, let’s break it up into 3 pieces and discuss them each below:

Toolbar / Action Buttons

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  • The name field tells you which matrix is currently being edited. This can make or break an experimental analysis that spans multiple runs, we recommend using a strict naming convention for your matrices to aid in identifying which data set they belong to.
  • The Edit button will duplicate the selected matrix and allow you to edit the compensation spillover values.
  • The [M] provides the capability to apply the current selected matrix to a sample or group by dragging and dropping.

The Matrix

  • The checkboxes on the left control which parameters are being used in the display portion (section 3 below). You can uncheck some parameters and then use the “show all” checkbox on top to hide unchecked parameters.
  • The numbers correspond to the spill values between two parameters. You can click inside a field and use up/down arrows to change the numbers. Modifier keys can be used to accelerate the change – hold down [ctrl], or [shift], or [alt] for finer/coarser changes.
  • The color coding is a simple heat map – blues are negative spills, and the increasingly darker shades of yellow are applied to higher values. You can use the heatmap to quickly identify the highest/lowest spills of your matrix, which can be useful to track down compensation problems.

Preview Area:

  • This view will show current sample’s fluorescent parameters in a grid of either histograms (ALLBY) or NxN bivariate plots. Note the heatmap from the matrix is retained here as background of each plot.
  • Checking the “Overlay Uncompensated” checkbox will paint a second layer on each plot that is the uncompensated parameters. This way you can see the difference before/after compensation.

ONE FINAL NOTE

If you need to create a blank matrix, simply click the plus (+) sign at the bottom of the matrix list:

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This will create an empty matrix that you can enter in values and apply to your samples:

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Return to Compensation Overview