QUALITY CONTROL

Generating high quality microarray data requires vigorous quality control measures at each individual step of the process, starting with the experimental design of the study, the generation of samples, extraction of RNA, labeling of the probe, and microarray hybridization. To minimize experimental variability, the same dedicated Research Assistants should perform all microarray studies, the same Affymetrix setup is used for hybridization, washing, and scanning, and microarrays of the same production lot are being used in comparative studies. For the following tutorial R and library affyQC was used to demonstrate the steps of Quality Control over Affymetrix chips.