Abstract: The methods provided focus on a quantitative molecular assay tools that systematically measure a set of pre-selected targets, with proper controls in a biological sample for identification of biomarkers or novel targets for a disease status. This allows for systematically maximizing the power of multivariate feature selection tools on the analysis of high-throughput screening data (such as microarray) and use of the well selected target to generate a qPCR array with tissue specific controls and qPCR controls to serve the needs of biomarker study.