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Permutation-Based Pathway Testing Using The Super Learner Algorithm, Paul Chaffee, Alan E. Hubbard, Mark L. Van Der Laan
Permutation-Based Pathway Testing Using The Super Learner Algorithm, Paul Chaffee, Alan E. Hubbard, Mark L. Van Der Laan
U.C. Berkeley Division of Biostatistics Working Paper Series
Many diseases and other important phenotypic outcomes are the result of a combination of factors. For example, expression levels of genes have been used as input to various statistical methods for predicting phenotypic outcomes. One particular popular variety is the so-called gene set enrichment analysis (GSEA). This paper discusses an augmentation to an existing strategy to estimate the significance of an associations between a disease outcome and a predetermined combination of biological factors, based on a specific data adaptive regression method (the "Super Learner," van der Laan et al., 2007). The procedure uses an aggressive search procedure, potentially resulting in …