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Permutation - based statistical tests for multiple hypotheses.

Camargo A, Azuaje F, Wang H, Zheng H - Source Code Biol Med (2008)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: University of Ulster at Jordanstown, School of Computing and Mathematics, Shore Road, Newtownabbey, Co, Antrim, BT37 0QB, Northern Ireland, UK. hy.wang@ulster.ac.uk.

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.

No MeSH data available.


Algorithm for multiple testing correction based on permutation test. Algorithm for multiple testing correction based on permutation test. Significance level (α), number of permutations(B), counter (T(per)), number of features (F), test statistic original data (T(obs)), test statistic permutated dataset (T(obs)').
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Figure 3: Algorithm for multiple testing correction based on permutation test. Algorithm for multiple testing correction based on permutation test. Significance level (α), number of permutations(B), counter (T(per)), number of features (F), test statistic original data (T(obs)), test statistic permutated dataset (T(obs)').

Mentions: Figure 3 is a pseudo-code representation of the multiple testing correction procedure implemented.


Permutation - based statistical tests for multiple hypotheses.

Camargo A, Azuaje F, Wang H, Zheng H - Source Code Biol Med (2008)

Algorithm for multiple testing correction based on permutation test. Algorithm for multiple testing correction based on permutation test. Significance level (α), number of permutations(B), counter (T(per)), number of features (F), test statistic original data (T(obs)), test statistic permutated dataset (T(obs)').
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2611984&req=5

Figure 3: Algorithm for multiple testing correction based on permutation test. Algorithm for multiple testing correction based on permutation test. Significance level (α), number of permutations(B), counter (T(per)), number of features (F), test statistic original data (T(obs)), test statistic permutated dataset (T(obs)').
Mentions: Figure 3 is a pseudo-code representation of the multiple testing correction procedure implemented.

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: University of Ulster at Jordanstown, School of Computing and Mathematics, Shore Road, Newtownabbey, Co, Antrim, BT37 0QB, Northern Ireland, UK. hy.wang@ulster.ac.uk.

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.

No MeSH data available.