Analyzing high-density oligonucleotide gene expression array data

We have developed methods and identified problems associated with the analy sis of data generated by high-density, oligonuceotide gene expression array s. Our methods are aimed at accounting for many of the sources of variation that make it difficult, at times, to realize consistent results. We presen t here descriptions of some of these methods and how they impact the analys is of oligonucleotide gene expression array data. We will discuss the proce ss of recognizing the "spots" (or features) on the Affymetrix GeneChip(R) p robe arrays, correcting for background and intensity gradients in the resul ting images, scaling/normalizing an array to allow array-to-array compariso ns, monitoring probe performance with respect to hybridization efficiency, and assessing whether a gene is present or differentially expressed. Exampl es from the analyses of gene expression validation data are presented to co ntrast the different methods applied to these types of data, J. Cell. Bioch em. 80.192-202, 2000. (C) 2000 Wiley-Liss, Inc.