How to calibrate Dues analog readings

Hello I am having problem with the analog readings on my due. On pin A4 and A5 am measuring the voltage

double vcc = 3.288  // taken on pin 75 (ADVREF) ;

analogReadResolution(12);

result = analogRead(A4) * (vcc / 4095);   // result = 0.47+- 0.01      multi-meter reading = 0.429

result = analogRead(A5) * (vcc / 4095);   // result = 0.49+- 0.01      multi-meter reading = 0.555

As you may see i could not simply offset the value because the both have very different offset one is positive and the other is negative. Also the reading is off by 0.05v which is inaccurate for a 12bit ADC which offers 0.000805v resolution almost a 1000x inaccurate.

Is there any way to calibrate this more futher?