A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates

Background: Studies of differential expression that use Affymetrix GeneChip arrays are often carried out with a limited number of replicates. Reasons for this include financial considerations and limits on the available amount of RNA for sample preparation. In addition, failed hybridizations are not uncommon leading to a further reduction in the number of replicates available for analysis. Most existing methods for studying differential expression rely on the availability of replicates and the demand for alternative methods that require few or no replicates is high. Results: We describe a statistical procedure for performing differential expression analysis without replicates. The procedure relies on a Bayesian integrated approach (BGX) to the analysis of Affymetrix GeneChips. The BGX method estimates a posterior distribution of expression for each gene and condition, from a simultaneous consideration of the available probe intensities representing the gene in a condition. Importantly...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Anne-Mette K. Hein, Sylvia Richardson
• Keywords: Affymetrix GeneChip Arrays, Affymetrix Genechips, BMCBI 2006, Posterior Distributions