About the Matrix File:
The saved matrix file is written in standard XML and is based on standards developed by the Flow Informatics and Computational Cytometry Society. 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. Parameters/channels that are not in this list have not been compensated; parameters/channels in this list that are not in the sample are ignored. The names must match exactly; best practice is to use the names that appear in the $PnN keywords of the FCS file.
Each parameter used in the matrix is shown, with the spillover coefficients corresponding to each of the channels other parameters given. Thus, 0.1654 is the spillover coefficient between FITC and PE, or the amount of FITC signal in the PE channel for a FITC-stained cell; 0.0125 is the amount of the PE signal in the FITC channel for a PE-stained cell. In very rough terms, the 0.1654 corresponds to approximately 16.5% spillover (PE-%FITC).
Click here for instructions on modifying the matrix.
When you modify the matrix, the numbers are converted to give an estimation of the amount (percentage) of spillover into the other parameter.
For an overview of compensation, go here.
