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Is it possible to use the setChannel() command to switch between the inputs for the internal ADC of PIC18F4550 at the end of each conversion, e.g. from AN0 to AN1 and back, or register initialisation is required for input switch?

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You can write an interrupt routine to get the result, toggle between channels and start a new conversion using the A/D interrupt, or poll the GO/DONE bit and do the same thing.

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