from Martin A. Lee, David J. Squirrell and Dario L. Leslie writing in Real-Time PCR: Advanced Technologies and Applications:
A range of factors can cause false negative results in real-time PCR through effects on one or more of the reaction components. Consequently applications requiring a high level of confidence need to be designed to control for the occurrence of false negatives. Whilst an external, or batch, control is often used, the ideal control is an internal one included in the reaction cocktail in a multiplex assay. Here we discuss the application and development of molecular mimics as controls in real-time PCR and explain concepts and experimental considerations to aid in the optimisation of controlled multiplexed assays.
Further reading: Real-Time PCR: Advanced Technologies and Applications