Use of within-array replicate spots for assessing differential expression in microarray experiments

Motivation. Spotted arrays are often printed with probes in duplicate or triplicate, but current methods for assessing differential expression are not able to make full use of the resulting information. Usual practice is to average the duplicate or triplicate results for each probe before assessing differential expression. This loses valuable information about gene-wise variability. Results. A method is proposed for extracting more information from within-array replicate spots in microarray experiments by estimating the strength of the correlation between them. The method involves fitting separate linear models to the expression data for each gene but with a common value for the between-replicate correlation. The method greatly improves the precision with which the genewise variances are estimated and thereby improves inference methods designed to identify differentially expressed genes. The method may be combined with empirical Bayes methods for moderating the genewise variances betw...

• Type: Journal
• Year: 2005
• Where: BIOINFORMATICS
• Authors: Gordon K. Smyth, Joëlle Michaud, Hamish S. Scott
• Keywords: BIOINFORMATICS 2005, Empirical Bayes, Expressed Genes, Ratio Control Spots