Set your default preferences for compensation

Select the Compensation button in the Preferences tool to open the Compensation preferences. The interface will open as shown below:


Compensation Group Inclusion
The “Group Inclusion” can be used to make files with certain file names get automatically included in the group when they are loaded into FlowJo.

$FIL – is the FCS file keyword for the name of the data file written by the cytometer.  The default values set are “comp” and “unstained”. Thus, any FCS files put into a workspace that contains the text “comp” or “unstained” in the $FIL, or filename, will be included in the compensation group in your workspace when loaded.

If you prefer to use a different keyword, you can remove the default $FIL strings using the X icon next to them in this interface and then click the “Add” button to add whatever keywords you would like to use. Some other common keywords are “TUBENAME” and “SampleID”.

These preferences can be very useful since you have the control to set the default values of whatever keyword you wish to automatically assign compensation single stain controls to the compensation group upon loading the files!

Matrix Editor

Link to the matrix editor

Confirm Edit – when you click the “Edit” button in the matrix editor, a confirmation box will open asking you to confirm that you wish to edit the matrix. If you prefer to not see this confirmation box, uncheck the box here in the preferences.

Overlay uncompensated – The matrix editor will allow you to overlay your uncompensated data on top of the compensated to view the difference. If you would like the uncompensated always overlaid by default, check this box in the preferences.