Preprocessing of Affymetrix Exon Expression Arrays

Abstract

The activity of genes can be captured by measuring the amount of messenger RNAs transcribed from the genes, or from their subunits called exons. In our study, we use the Affymetrix Human Exon ST v1.0 micro arrays to measure the activity of exon s in Neuroblastoma cancer patients. The purpose is to discover a small number of genes or exons that play important roles in differentiating high - risk patients fro m low - risk counterparts. Although the technology has been improved for the past 15 years, array measurements still can be contaminated by various factors, including human error. Since the number of arrays is often only few hundreds, atypical errors can hardly be canceled by large numbers of normal arrays. In this article we describe how we filter out low - quality arrays in a principled way, so that we can obtain more reliable results in downstream analyses.