Compensation: The gruesome details

This series of pages is designed to give a much more complete overview of compensation than the informal discussion. It contains examples as well as mathematical treatments necessary to understand compensation thoroughly. It also covers the pitfalls of compensation, and details some of the more esoteric points that are involved in the process. To reference any of this material, see the introduction to the informal discussion.

Currently, there is no way to download the complete set of these pages at once, for printing.

These pages are designed to be navigated in order; however, you can jump directly to some of the sections (marked with an *) without losing too much from previous pages.

Begin with the gruesome details!

* Why do we need Compensation?
How does compensation work? (One-way)
How does compensation work? (Two-way)
A mathematical example of 2-way compensation
Three-color compensation
* Generalized compensation (n-colors)
Autofluorescence
* Requirements for proper compensation
Co-stained compensation samples
* 2-color compensation: examples (& what to look for)
An example of improper 3-color compensation
* Errors introduced by compensation
Postscript
References

Compensation FAQ

Fluorescence spectra of fluorescein, PE, and Cy5PE
Fluorescein emissions into different channels
PE emission into different channels
Compensation of dim and bright stains
Example of 2-color compensation (right and wrong)
Example of 3-color compensation (right and wrong)