A method of performing a multiplexed digital assay, the method comprising: providing a mixture including a plurality of targets and reagents sufficient for amplification of each of the targets, wherein the plurality of targets includes a first target and a second target; forming partitions each including a portion of the mixture; amplifying the plurality of targets in the partitions; collecting data from a plurality of the partitions for amplification of each of the plurality of targets; identifying a partition population positive for neither the first target nor the second target, a partition population positive for the first target but not the second target, and a mixed population including a pair of partition populations that are not resolved from one another in the data, the pair of partition populations being a population of partitions positive for the second target but not the first target and a population of partitions positive for both the first target and the second target, wherein a presence of the second target at least partially masks a presence of the first target in the data for a plurality of the partitions each containing at least one copy of each target; and calculating a level of the first target from only a portion of the data, wherein the portion of the data is collected from only a subset of the plurality of the partitions and excludes each partition testing positive for the second target; wherein the method further comprises a step of obtaining a total partition count and a first-target-related partition count from the subset of partitions, wherein the first-target-related partition count is a number of partitions positive for the first target in the subset of partitions or a number of partitions negative for the first target in the subset of partitions, and wherein the step of calculating a level is performed with the total partition count and the first-target-related partition count to calculate a concentration of the first target. providing a mixture including a plurality of targets and reagents sufficient for amplification of each of the targets, wherein the plurality of targets includes a first target and a second target; forming partitions each including a portion of the mixture; amplifying the plurality of targets in the partitions; collecting data from a plurality of the partitions for amplification of each of the plurality of targets; identifying a partition population positive for neither the first target nor the second target, a partition population positive for the first target but not the second target, and a mixed population including a pair of partition populations that are not resolved from one another in the data, the pair of partition populations being a population of partitions positive for the second target but not the first target and a population of partitions positive for both the first target and the second target, wherein a presence of the second target at least partially masks a presence of the first target in the data for a plurality of the partitions each containing at least one copy of each target; and calculating a level of the first target from only a portion of the data, wherein the portion of the data is collected from only a subset of the plurality of the partitions and excludes each partition testing positive for the second target; wherein the method further comprises a step of obtaining a total partition count and a first-target-related partition count from the subset of partitions, wherein the first-target-related partition count is a number of partitions positive for the first target in the subset of partitions or a number of partitions negative for the first target in the subset of partitions, and wherein the step of calculating a level is performed with the total partition count and the first-target-related partition count to calculate a concentration of the first target.