The article by Gordon K. Smyth and Terry Speed discusses the normalization of cDNA microarray data to adjust for variations in the technology rather than biological differences. The authors describe several normalization methods, including print-tip loess normalization, which is a well-tested method that corrects for intensity and spatial trends. They also introduce composite loess normalization, which uses control spots known to be non-differentially expressed, and scale normalization between arrays to address differences in scanner settings or print quality. The article emphasizes the importance of diagnostic plots to visualize intensity and spatial trends and provides detailed commands for implementing these normalization techniques using freely available software. The authors conclude that print-tip loess normalization is a robust and effective method for cDNA microarray data normalization, with potential refinements through the use of quality weights and further diagnostic analysis.The article by Gordon K. Smyth and Terry Speed discusses the normalization of cDNA microarray data to adjust for variations in the technology rather than biological differences. The authors describe several normalization methods, including print-tip loess normalization, which is a well-tested method that corrects for intensity and spatial trends. They also introduce composite loess normalization, which uses control spots known to be non-differentially expressed, and scale normalization between arrays to address differences in scanner settings or print quality. The article emphasizes the importance of diagnostic plots to visualize intensity and spatial trends and provides detailed commands for implementing these normalization techniques using freely available software. The authors conclude that print-tip loess normalization is a robust and effective method for cDNA microarray data normalization, with potential refinements through the use of quality weights and further diagnostic analysis.