Compensation FAQ

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.

Note, Compensation should always be preceded by scaling your data appropriately. Poorly scaled data will effect downstream compensation, so get into the habit of adjusting transforms through the “T” button in FlowJo’s graph window, prior to opening the compensation wizard for single stained control assignment.

CHAPTER 1 – Altering an acquisition matrix

Many data files contain their own pre-defined compensation matrix keyword, which was written when the file was created. This keyword is read and data in the file are compensated when the data is read into FlowJo. If, for any reason, you want to alter the matrix values, read this chapter.


CHAPTER 2 – Creating a FlowJo compensation matrix from single stain controls

If you acquired your data with single-stain controls and wish to compensate it using FlowJo, read this chapter.


CHAPTER 3 – The Matrix Editor

Once you have a compensation matrix and wish to examine it, you will be using the Matrix Editor. To familiarize yourself with this interface, read this chapter.