The digital array has the ability to absolutely quantitate any type of DNA sample. In a multiplex PCR reaction with two assays, the quantitation of two or more genes/sequences in a single sample becomes possible, effectively eliminating pipetting variations inherently occurring in any quantitation experiment. The accuracy of the results is only subject to the random distribution of the molecules and, like any biological experiments, can improve with the use of multiple replicates for each sample. STA can efficiently separate the linked copies of a gene on the same chromosome when duplication occurs while other methods, such as restriction digestion are also valid (data not shown).