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Unexpected behaviour when testing for independence, with multiple factors

I tried what you suggested Ben, but I'm still puzzled by the output.
In this case, I obtain different results with different ordering of
the factors:
Fligner-Killeen test of homogeneity of variances

data:  dT by Dims by Topology by Drift
Fligner-Killeen:med chi-squared = 195.2067, df = 1, p-value < 2.2e-16
Fligner-Killeen test of homogeneity of variances

data:  dT by Topology by Drift by Dims
Fligner-Killeen:med chi-squared = 15.4343, df = 2, p-value = 0.0004451


I don't know what to do now, any help would be reaaally appreciated.

Best Regards
Javier

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Javier Acuna
Electrical Engineering Grad Student
Universidad de Chile
javier.acuna.o at gmail.com