Analysis of oligonucleotide data with a view to data quality assessment

High density oligonucleotide arrays are widely used in many areas of biomedical research to perform quantitative and highly parallel measurements of gene expression. The most popular of these technologies are the Affymetrix GeneChipRTM arrays. The technology enables researchers to detect and quantify tens of thousands of transcripts in a single experiment and can be used to discover gene functions, to evaluate potential drugs and therapies, to dissect genetic pathways, and to classify clinical samples.; This new technology produces amounts of genetic information never encountered before. Although the quantities of data requiring analysis in a typical experiment has reached new scales, the statistical and analytical problems are not new. We use traditional statistical methods to derive a model for oligo array data which can be used to answer the basic questions regarding gene expression. The model also provides a means of assessing the success of a microarray experiment with respect to the quality of the gene expression measures that are computed from the array data. We derive quality assessment measures which improve upon current standards.