The invention provides methods of conducting a nucleic acid reaction, including methods for performing digital PCR using a “droplet-in-oil” technology. In the methods, the starting sampled is segmented at least partially into a set of sample droplets each containing on average about one or fewer copies of a target nucleic acid. The droplets are passed in a continuous flow of immiscible carrier fluid through a channel that passes through a thermal cycler, whereby the target is amplified. In one implementation, the droplets are about 350 nl each and the number of positively amplified droplets is counted at the near-saturation point.