CNV determination on the digital array is based upon its ability to partition DNA sequences. Given the number of molecules per panel and the dilution factor, the concentration of the target sequence in a DNA sample can be accurately calculated. In a multiplex PCR reaction with 2 or more assays, multiple genes can be quantitated simultaneously and independently, effectively eliminating any pipetting errors if separate reactions have to be set up for different genes. When a single copy reference gene (RNase P in this study, [10] ) is used in the reaction, the ratio of the target gene to the reference gene would reflect the copy number per haploid genome of the target gene. Primary contribution of this paper In this paper we will show that the digital array provides a robust and easy-to-use platform to study CNVs. We have derived a mathematical framework to calculate the true concentration of molecules from the observed positive reactions in a panel. We also show how to perform statistical analysis to find the 95% confidence intervals of the true concentrations and the ratio of two concentrations in a CNV experiment using the digital array with multiplex PCR.