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In the Rydberg equation, n1 and n2 are whole integers from 1 to infinity where n2 > n1. You can also call n1 the initial energy level, for example for the Balmer series, it would be n1=2 and n2 would be any value greater than 2.
I'm not sure if this answers your question, but it is always going to be final - initial. So I believe in the Rydberg equation you wrote out, n1 would be final and n2 would be the initial.
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