simulate this circuitsimulate this circuit – Schematic created using CircuitLab
If you look at the ATMega328p datasheet you'll see that the ADC only supports single ended voltage measurements. For some other Atmel chips (search for "23e.2 Analog Comparator Multiplexed Input"g. the ATTiny45) you'll see that you can change the negative pin used by the ADC by setting the ADMUX register. For instance
ADMUX =|= _BV(MUX0);
should set ADC1 as the negative input.
If you look at the Arduino source for analogRead (notewiring_analog.c) you'll see that youthis method resets the ADMUX register so you'd have to first disable the ADC beforewrite your own function if you can change this value). What's curious from an Arduino Uno standpoint is that AIN1 is the negative by default which is digital pin 7 on an Uno. I'm not sure howwanted to use a differential measurement using a chip that is handled by the Arduino's analogRead functionsupported it.