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 Error in the compensation matrix
Compensation matrix does not apply to sample

The compensation matrix you tried to apply to the sample was created for samples with completely different parameter names. FlowJo stores the parameter names in the compensation matrix itself, so that the coefficients will be applied to the appropriate parameters.

Since the matrix was created for different parameter names, it is probably not appropriate that it be applied to this sample. Nonetheless, if you wish, you can edit the matrix file and replace the existing parameter names with the parameter names that are in the file you are trying to compensate. The parameter names are the values for the $PnN keywords (i.e., they are not the stain names).

You should only try to edit the compensation matrix if you know exactly what you are doing. You can get more information about compensation in general, or specifically about modifying the compensation matrix manually.

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