ABSTRACT
This chapter defines dynamic range as the range of message abundance that can be robustly detected in the target, ranging from the lowest abundance message that produces a hybridization signal just above background levels up to the highest abundance message that saturates the response of the array. Widespread application of common Quality Control (QC) methods is crucial to achieving comparable data, and this has been recognized in community database initiatives such as Minimum information about a microarray experiment. The majority of the authors’ experience has been with the Affymetrix GeneChip™ oligonucleotide array platform. The chapter describes QC methods that can be applied directly to this platform. To validate the performance of an array, independent of possible sample-related QC problems, spiking of labeled control transcripts into copy-RNA is a very useful method. Visual inspection of the array image is the most basic, and effective, QC method.
