Extraction of Differential Gene Expression

EDGE is a software package for the significance analysis of DNA microarray experiments
for both standard and time course experiments
based on our new Optimal Discovery Procedure and Time Course Methodology

Storey JD. (2007) The optimal discovery procedure: A new approach to simultaneous significance testing. Journal of the Royal Statistical Society, Series B, 69: 347-368. [PDF] [Web Site]
Storey JD, Dai JY, and Leek JT. (2007) The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments. Biostatistics, 8: 414-432. [PDF] [Web Site] [Supp Info]
Leek JT, Monsen EC, Dabney AR, and Storey JD. (2006) EDGE: Extraction and analysis of differential gene expression. Bioinformatics, 22: 507-508. [PDF]
Storey JD, Xiao W, Leek JT, Tompkins RG, and Davis RW. (2005) Significance analysis of time course microarray experiments. Proceedings of the National Academy of Sciences, 102: 12837-12842. [PDF] [Web Site]

Software based on statistical theory developed in the Storey Lab
Implements the new Optimal Discovery Procedure (ODP) -- click here for an explanation
Performs significance analysis of regular "snapshot" experiments
Performs significance analysis of time course experiments -- click here for an explanation
Identifies genes differentially expressed across distinct biological groups or with respect to a continuous variable
Accurately tests for over/under-expression and fold-change -- coming soon

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Software by Jeffrey Leek, Alan Dabney, Eva Monsen and John Storey.