Combining gene expression data from different generations of oligonucleotide arrays

Background: One of the important challenges in microarray analysis is to take full advantage of previously accumulated data, both from one's own laboratory and from public repositories. Through a comparative analysis on a variety of datasets, a more comprehensive view of the underlying mechanism or structure can be obtained. However, as we discover in this work, continual changes in genomic sequence annotations and probe design criteria make it difficult to compare gene expression data even from different generations of the same microarray platform. Results: We first describe the extent of discordance between the results derived from two generations of Affymetrix oligonucleotide arrays, as revealed in cluster analysis and in identification of differentially expressed genes. We then propose a method for increasing comparability. The dataset we use consists of a set of 14 human muscle biopsy samples from patients with inflammatory myopathies that were hybridized on both HG-U95Av2 a...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Kyu Baek Hwang, Sek Won Kong, Steven A. Greenberg, Peter J. Park
• Keywords: Analysis, BMCBI 2004, Comparative Analysis, Expression Values