Procedures with true discovery guarantee, i.e., methods for simultaneous inference on the True Discovery Proportion (TDP), have become widely popular in many applications. They permit addressing the multiplicity problem while at the same time solving the spatial specificity paradox. Here we propose a comparative analysis of some of the most widely used permutation-based procedures: sumSome, pARI, sansSouci and Notip. We compare their performance on differential gene expression data analysis, where the interest lies in quantifying levels of activation in different pathways.
How active is a genetic pathway? Comparative analysis of post-hoc permutation-based methods
Angela Andreella
2023-01-01
Abstract
Procedures with true discovery guarantee, i.e., methods for simultaneous inference on the True Discovery Proportion (TDP), have become widely popular in many applications. They permit addressing the multiplicity problem while at the same time solving the spatial specificity paradox. Here we propose a comparative analysis of some of the most widely used permutation-based procedures: sumSome, pARI, sansSouci and Notip. We compare their performance on differential gene expression data analysis, where the interest lies in quantifying levels of activation in different pathways.
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