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Updated: May 21, 2026

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
Published on: November 3, 2010
Detecting differentially expressed genes in heterogeneous diseases using control-only analysis of variance
I-Shiang Tzeng1, Wen-Chung Lee
1Research Center for Genes, Environment and Human Health, College of Public Health, National Taiwan University, Taiwan.
Purpose:
Microarray technology allows for simultaneously screening many genes and determining which gene(s) are differentially expressed in different disease statuses or different cell types. The analysis of variance (ANOVA) (for a K-sample situation with K>2) can be used in such occasions to gauge statistical significances. However, the test may be underpowered if the diseases under study are heterogeneous.
Methods:
The authors propose the "control-only ANOVA" for detecting differentially expressed genes in heterogeneous diseases. Monte-Carlo simulation shows that the test produces quite accurate type I error rates for both normal and non-normal data. The statistical power of the control-only ANOVA is higher than that of the conventional ANOVA when the diseases under study are heterogeneous.
Results:
Analysis of a real data set shows that after Bonferroni correction, the control-only ANOVA detects three differentially expressed genes, whereas the conventional ANOVA can detect only one.
Conclusions:
The control-only ANOVA is recommended for use when the diseases under study are heterogeneous.
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