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The file generated by FlowJo in response to the "Compute" button in the compensation matrix dialog window is a text file. The compensation matrix file will contain mathematical information about how much to compensate each channel. In this example, the matrix may look like this:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE CompensationMatrix>
<CompensationMatrix name="compensation2.mtx" prefix="Comp-" suffix="" version="Version 5.3">
<Channel name="Fluor">
<ChannelValue name="Fluor" value="1.00000" />
<ChannelValue name="PhyEry" value="0.16476" />
<ChannelValue name="Cy5PE" value="0.03454" />
</Channel>
<Channel name="PhyEry">
<ChannelValue name="Fluor" value="0.01720" />
<ChannelValue name="PhyEry" value="1.00000" />
<ChannelValue name="Cy5PE" value="0.21598" />
</Channel>
<Channel name="Cy5PE">
<ChannelValue name="Fluor" value="0.00632" />
<ChannelValue name="PhyEry" value="0.23652" />
<ChannelValue name="Cy5PE" value="1.00000" />
</Channel>
</CompensationMatrix>

The first two lines have the XML declarations. The third line has the name of the compensation matrix, as well as the prefix and suffix.

The subsequent lines list channel names and spillover coefficients for each channel relative to other channels in that data file. Channels that are not in this list are not compensated; channels in this list that are not in the sample are ignored. The names must match exactly; use the names that appear in the $PnN keywords of the FCS file. The names are separated by tabs.

We do not recommend modifying the matrix file (this is why FlowJo doesn't have compensation "knobs"). However if you must...

When modifying the matrix file, do not change the formatting; make sure that the number of coefficients, names, and lines are correct as well as being tab-delimited.

Go back to the overview of compensation.

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