[11] Analysis of Variance of Microarray Data

Julien F. Ayroles, Greg Gibson

Research output: Contribution to journalReview articlepeer-review

29 Scopus citations


Analysis of variance (ANOVA) is an approach used to identify differentially expressed genes in complex experimental designs. It is based on testing for the significance of the magnitude of effect of two or more treatments taking into account the variance within and between treatment classes. ANOVA is a highly flexible analytical approach that allows investigators to simultaneously assess the contributions of multiple factors to gene expression variation, including technical (dye, batch) effects and biological (sex, genotype, drug, time) ones, as well as interactions between factors. This chapter provides an overview of the theory of linear mixture modeling and the sequence of steps involved in fitting gene-specific models and discusses essential features of experimental design. Commercial and open-source software for performing ANOVA is widely available.

Original languageEnglish (US)
Pages (from-to)214-233
Number of pages20
JournalMethods in enzymology
StatePublished - 2006

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Biochemistry


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