The ADC has two conversion options: differential and single-ended:
If the positive input is always positive, the single-ended conversion should be used in order to have full 12-bit resolution in the conversion.
If the positive input may go below the negative input, the differential mode should be used in order to get correct results.
The differential mode is enabled by setting DIFFMODE bit in the Control C register (CTRLC.DIFFMODE). Both conversion types could be run in single mode or in free-running mode. When the free-running mode is selected, an ADC input will continuously sample the input and performs a new conversion. The INTFLAG.RESRDY bit will be set at the end of each conversion.