• Journal of the Korean Data and Information Science Society
• /
• v.18 no.4
• /
• pp.1145-1155
• /
• 2007

In this paper, we consider the permutation tests for the multivariate data under the two-sample problem setting. We review some testing procedures, which are parametric and nonparametric and compare them with the permutation ones. Then we consider to try to apply the permutation tests to the multivariate data having the continuous and discrete components together by choosing some suitable combining function through the partial testing. Finally we discuss more aspects for the permutation tests as concluding remarks.

• Genomics & Informatics
• /
• v.20 no.1
• /
• pp.14.1-14.4
• /
• 2022

Permutation testing is a robust and popular approach for significance testing in genomic research that has the advantage of reducing inflated type 1 error rates; however, its computational cost is notorious in genome-wide association studies (GWAS). Here, we developed a supercomputing-aided approach to accelerate the permutation testing for GWAS, based on the message-passing interface (MPI) on parallel computing architecture. Our application, called MPI-GWAS, conducts MPI-based permutation testing using a parallel computing approach with our supercomputing system, Nurion (8,305 compute nodes, and 563,740 central processing units [CPUs]). For 10⁷ permutations of one locus in MPI-GWAS, it was calculated in 600 s using 2,720 CPU cores. For 10⁷ permutations of ~30,000-50,000 loci in over 7,000 subjects, the total elapsed time was ~4 days in the Nurion supercomputer. Thus, MPI-GWAS enables us to feasibly compute the permutation-based GWAS within a reason-able time by harnessing the power of parallel computing resources.

• Journal of the Korea Society of Computer and Information
• /
• v.27 no.6
• /
• pp.167-174
• /
• 2022

In this paper we investigate the permutation test for the equality of correlation coefficients in several independent populations. Permutation test is a non-parametric testing methodology based upon the exchangeability of observations. Exchangeability is a generalization of the concept of independent, identically distributed random variables. Using permutation method, we may construct asymptotically exact test. This method is asymptotically as powerful as standard parametric tests and is a valuable tool when the sample sizes are small and normality assumption cannot be met. We first review existing parametric approaches to test the equality of correlation coefficients and compare them with the permutation test. At the end, all the approaches are illustrated using Iris data example.

• Journal of the Korea Society of Computer and Information
• /
• v.26 no.8
• /
• pp.157-164
• /
• 2021

Regression analysis is a well-known statistical technique useful to explain the relationship between response variable and predictor variables. In particular, Researchers are interested in comparing the regression coefficients(intercepts and slopes) of the models in two independent populations. The Chow test, proposed by Gregory Chow, is one of the most commonly used methods for comparing regression models and for testing the presence of a structural break in linear models. In this study, we propose the use of permutation method and compare it with Chow test analysis for testing the equality of two independent linear regression models. Then simulation study is conducted to examine the powers of permutation test and Chow test.

• The Korean Journal of Applied Statistics
• /
• v.31 no.2
• /
• pp.241-251
• /
• 2018

The analysis of gene sets in microarray has advantages in interpreting biological functions and increasing statistical powers. Many statistical methods have been proposed for detecting significant gene sets that show relations between genes and phenotypes, but there is no consensus about which is the best to perform gene sets analysis and permutation based tests are considered as standard tools. When many gene sets are tested simultaneously, a large number of random permutations are needed for multiple testing with a high computational cost. In this paper, several parametric approximations are considered as alternatives of the permutation distribution and the moment based gene set test has shown the best performance for providing p-values of the permutation test closely and quickly on a general framework.

• Journal of the Korea Society of Computer and Information
• /
• v.24 no.6
• /
• pp.159-164
• /
• 2019

The statistical inference of Cronbach's alpha measure of internal reliability is known to be inaccurate when sample size is small and the assumption of normality is violated. In this paper, we describe the permutation method in which we compute resampling p-values for testing the difference between two or more independent Cronbach's alpha coefficients. When the over-all permutation test is significant, we also make pairwise post-hoc comparisons using permutaion method. The permutation tests for the equality of two independent Cronbach's alpha coefficients and three independent Cronbach's alpha coefficients are illustrated with an example analysis of survey data.

• Communications for Statistical Applications and Methods
• /
• v.11 no.3
• /
• pp.657-668
• /
• 2004

Permutation test has been applied for the QTL(quantitative trait loci) analysis and we selected a major locus. K -means clustering analysis, for the major DNA Marker mining of ILSTS035 microsatellite loci in Hanwoo chromosome 6, has been described. Finally, bootstrap testing method has been adapted to calculate confidence intervals and for finding major DNA Markers.

• Journal of the Korea Academia-Industrial cooperation Society
• /
• v.14 no.3
• /
• pp.1451-1458
• /
• 2013

This paper deals with the programs and algorithms that generate the full data set that satisfy the basic combinatorial requirement of combination, permutation, partial permutation or shortly r-permutation, which are used in the application of the total data testing or the simulation input. We search the programs able to meet the rules which is permutations and combinations, r-permutations, select the fastest program by field. With further study, we developed a new program reducing the time required to processing. Our research performs the following pre-study. Firstly, hundreds of algorithms and programs in the internet are collected and corrected to be executable. Secondly, we measure running time for all completed programs and select a few fast ones. Thirdly, the fast programs are analyzed in depth and its pseudo-code programs are provided. We succeeded in developing two programs that run faster. Firstly, the combination program can save the running time by removing recursive function and the r-permutation program become faster by combining the best combination program and the best permutation program. According to our performance test, the former and later program enhance the running speed by 22% to 34% and 62% to 226% respectively compared with the fastest collected program. The programs suggested in this study could apply to a particular cases easily based on Pseudo-code., Predicts the execution time spent on data processing, determine the validity of the processing, and also generates total data with minimum access programming.

• The Korean Journal of Applied Statistics
• /
• v.22 no.5
• /
• pp.1097-1102
• /
• 2009

Classification of subjects with unknown distribution in small sample size setup may involve order-restricted constraints in multivariate parameter setups. Those problems makes optimality of conventional likelihood ratio based statistical inferences not feasible. Fortunately, Roy (1953) introduced union-intersection principle(UIP) which provides an alternative avenue. Redescending M-estimator along with that principle yields a considerably appropriate robust testing procedure. Furthermore, conditionally distribution-free test based upon exact permutation theory is used to generate p-values, even in small sample. Applications of this method are illustrated in simulated data and read data example (Lobenhofer et al., 2002)

• The Korean Journal of Applied Statistics
• /
• v.24 no.1
• /
• pp.137-143
• /
• 2011

The classification of subjects with unknown distribution in a small sample size often involves order-restricted constraints in multivariate parameter setups. Those problems make the optimality of a conventional likelihood ratio based statistical inferences not feasible. Fortunately, Roy (1953) introduced union-intersection principle(UIP) which provides an alternative avenue. Multivariate linear rank statistics along with that principle, yield a considerably appropriate robust testing procedure. Furthermore, conditionally distribution-free test based upon exact permutation theory is used to generate p-values, even in a small sample. Applications of this method are illustrated in a real microarray data example (Lobenhofer et al., 2002).