Issue No. 03 - July-September (2008 vol. 5)
A principal goal of microarray studies is to identify the genes showing differential expression under distinct conditions. In such studies, the selection of an optimal test statistic is a crucial challenge, which depends on the type and amount of data under analysis. While previous studies on simulated or spike-in datasets do not provide practical guidance on how to choose the best method for a given real dataset, we introduce an enhanced reproducibility-optimization procedure, which enables the selection of a suitable gene- anking statistic directly from the data. In comparison with existing ranking methods, the reproducibilityoptimized statistic shows good performance consistently under various simulated conditions and on Affymetrix spike-in dataset. Further, the feasibility of the novel statistic is confirmed in a practical research setting using data from an in-house cDNA microarray study of asthma-related gene expression changes. These results suggest that the procedure facilitates the selection of an appropriate test statistic for a given dataset without relying on a priori assumptions, which may bias the findings and their interpretation. Moreover, the general reproducibilityoptimization procedure is not limited to detecting differential expression only but could be extended to a wide range of other applications as well.
Microarray, gene expression, gene ranking, reproducibility, differential expression, bootstrap
S. Filén, T. Aittokallio, R. Lahesmaa and L. L. Elo, "Reproducibility-Optimized Test Statistic for Ranking Genes in Microarray Studies," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 5, no. , pp. 423-431, 2007.