MAANOVA: A Software Package for the Analysis of Spotted cDNA Microarray Experiments. We describe a software package called MAANOVA (MicroArray ANalysis Of VAriance). MAANOVA is a collection of functions for statistical analysis of gene expression data from two-color cDNA microarray experiments. It is available in both the Matlab and R programming environments and can be run on any platform that supports these packages. MAANOVA allows the user to assess data quality, apply data transformations, estimate relative gene expression from designed experiments with ANOVA models, evaluate and interpret ANOVA models, formally test for differential expression of genes and estimate false-discovery rates, produce graphical summaries of expression patterns, and perform cluster analysis with bootstrapping. The development of MAANOVA was motivated by the need to analyze microarray data that arise from sophisticated designed experiments. MAANOVA provides specialized functions for microarray analysis in an open-ended format within flexible computing environments. MAANOVA functions can be used alone or in co mbination with other functions for the rigorous statistical analysis of microarray data

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