Software review

Permutation – based statistical tests for multiple hypotheses

Anyela Camargo¹ , Francisco Azuaje² , Haiying Wang³ and Huiru Zheng³

¹  University of East Anglia, School of Computing, Norwich, NR4 7TJ, England, UK

²  Laboratory of Cardiovascular Research, CRP-Santé, L-1150, Luxembourg

³  University of Ulster at Jordanstown, School of Computing and Mathematics, Shore Road, Newtownabbey, Co. Antrim, BT37 0QB, Northern Ireland, UK

author email corresponding author email

Source Code for Biology and Medicine 2008, 3:15doi:10.1186/1751-0473-3-15

Published:	21 October 2008

Abstract

Background

Genomics and proteomics analyses regularly involve the simultaneous test of hundreds of hypotheses, either on numerical or categorical data. To correct for the occurrence of false positives, validation tests based on multiple testing correction, such as Bonferroni and Benjamini and Hochberg, and re-sampling, such as permutation tests, are frequently used. Despite the known power of permutation-based tests, most available tools offer such tests for either t-test or ANOVA only. Less attention has been given to tests for categorical data, such as the Chi-square. This project takes a first step by developing an open-source software tool, Ptest, that addresses the need to offer public software tools incorporating these and other statistical tests with options for correcting for multiple hypotheses.

Results

This study developed a public-domain, user-friendly software whose purpose was twofold: first, to estimate test statistics for categorical and numerical data; and second, to validate the significance of the test statistics via Bonferroni, Benjamini and Hochberg, and a permutation test of numerical and categorical data. The tool allows the calculation of Chi-square test for categorical data, and ANOVA test, Bartlett's test and t-test for paired and unpaired data. Once a test statistic is calculated, Bonferroni, Benjamini and Hochberg, and a permutation tests are implemented, independently, to control for Type I errors. An evaluation of the software using different public data sets is reported, which illustrates the power of permutation tests for multiple hypotheses assessment and for controlling the rate of Type I errors.

Conclusion

The analytical options offered by the software can be applied to support a significant spectrum of hypothesis testing tasks in functional genomics, using both numerical and categorical data.