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The LeFE algorithm: embracing the complexity of gene expression in the interpretation of microarray data
Gabriel S Eichler, Mark Reimers, David Kane and John N Weinstein
Genome Biol. 2007 Sep 10;8(9):R187
Abstract:
Interpretation of microarray data remains a challenge, and most methods fail to consider the complex, nonlinear regulation of gene
expression. To address that limitation, we introduce Learner of Functional Enrichment (LeFE), a statistical/machine learning algorithm based on
Random Forest, and demonstrate it on several diverse datasets: smoker/never smoker, breast cancer classification, and cancer drug sensitivity.
We also compare it with previously published algorithms, including Gene Set Enrichment Analysis. LeFE regularly identifies statistically significant
functional themes consistent with known biology.
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