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The RMM values are sometimes quite different. Can I average the values of RMM1 and RMM2 and use it as an index for MJO?

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CAN you? Sure, nobody on here is stopping you.

Is it meaningful? Not really.

The RMM indices are two separate metrics corresponding to the phase (interpretable using a phase space diagram)

MJO Phase Space Diagram

(Example from CPC)

If you want a more meaningful way to interpret the MJO, you can try $$\sqrt{RMM_1^2+RMM_2^2}$$ which should be the strength of the MJO, or the angle between $RMM_1$ and $RMM_2$ (probably using something like atan2 in your preferred programming language.

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