Microarray has revolutionized the study of molecular biology, especially the application in clinical diagnostics. When used in clinical diagnostics, microarray has to meet a high degree of reproducibility, reliability and quality in order to become a standard tool. Repeatability and reproducibility are essential for providing the best data and process control. The real challenge for microarray is, however, how to produce consistent and reliable data. The variance of microarray data is contributed by the quality of sample source, the quality of glass substrates, hybridization, and probe labeling and spotting. The quality of coated glass substrates is one of the main factors. This paper is focusing on discussing how to optimize coating conditions to improve the slide quality, consequently improve the data quality such as sensitivity and data reliability.