http://www.ncgc.nih.gov/guidance/section3.html
Key assays in a project and assays where problems are suspected should have two control compounds, a primary and a secondary (this is referred to as Close Monitoring). All other assays should have at least a primary control (Regular Monitoring). Both compounds need to be run once per run, unless plate variability is suspected. In that case the primary control compound needs to be run once per plate. The purpose of the primary control is to ensure that there isn�t any �assay drift�, i.e. that the same compound has a stable Ki/Kb/EC50 over time, and that the assay reproducibility (MSR) is stable over time.