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we had 2 wheels and hence 2 encoders. Would that cause any problems?
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No. (But see the following note about wiring).
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also, I am not sure how much to be worried about the singal integrity over the 7 feet of wire that the students had wired next to all other wires.
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You should be worried enough to test the sensor signals thoroughly before trying to tune the control algorithm. But then again, it's proper practice to do that anyway.
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including the 20kHz jaguar output wires going to the motors
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For the record, Jag PWM frequency is 15KHz.