Transgenes can be inserted as tandem copies (multiple copies in a row) in the genome. For digital PCR quantification, it is crucial that the different copies are detached from each other; each reaction should receive just one copy, otherwise, you underestimate the transgene copy number. There is a presentation on the Biogazelle website about digital PCR based transgene quantification.

http://www.biogazelle.com/knowledge-center/presentations