The Annals of Applied Statistics

Testing the disjunction hypothesis using Voronoi diagrams with applications to genetics

Daisy Phillips and Debashis Ghosh

Full-text: Open access

Abstract

Testing of the disjunction hypothesis is appropriate when each gene or location studied is associated with multiple $p$-values, each of which is of individual interest. This can occur when more than one aspect of an underlying process is measured. For example, cancer researchers may hope to detect genes that are both differentially expressed on a transcriptomic level and show evidence of copy number aberration. Currently used methods of $p$-value combination for this setting are overly conservative, resulting in very low power for detection. In this work, we introduce a method to test the disjunction hypothesis by using cumulative areas from the Voronoi diagram of two-dimensional vectors of $p$-values. Our method offers much improved power over existing methods, even in challenging situations, while maintaining appropriate error control. We apply the approach to data from two published studies: the first aims to detect periodic genes of the organism Schizosaccharomyces pombe, and the second aims to identify genes associated with prostate cancer.

Article information

Source
Ann. Appl. Stat., Volume 8, Number 2 (2014), 801-823.

Dates
First available in Project Euclid: 1 July 2014

Permanent link to this document
https://projecteuclid.org/euclid.aoas/1404229515

Digital Object Identifier
doi:10.1214/13-AOAS707

Mathematical Reviews number (MathSciNet)
MR3262535

Zentralblatt MATH identifier
06333777

Keywords
Multiple testing false discovery rates Voronoi tessellations empirical null distributions

Citation

Phillips, Daisy; Ghosh, Debashis. Testing the disjunction hypothesis using Voronoi diagrams with applications to genetics. Ann. Appl. Stat. 8 (2014), no. 2, 801--823. doi:10.1214/13-AOAS707. https://projecteuclid.org/euclid.aoas/1404229515


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Supplemental materials

  • Supplementary material A: Summarized results of additional simulation studies. We present the summarized results of the proposed procedure’s performance in the challenging situations described in Section 7. Results include estimated FDR and 1-NDR for each of the two settings.
  • Supplementary material B: Supplementary code and data. R code including the functions required to perform the procedure described in this paper, to replicate the described simulation studies and to perform the described data analysis. The relevant data sets are also included.