An adaptive two-sample test for high-dimensional means.
Ontology highlight
ABSTRACT:
SUBMITTER: Xu G
PROVIDER: S-EPMC5549874 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:We develop a test statistic for testing the equality of two population mean vectors in the "large-p-small-n" setting. Such a test must surmount the rank-deficiency of the sample covariance matrix, which breaks down the classic Hotelling T2 test. The proposed procedure, called the generalized component test, avoids full estimation of the covariance matrix by assuming that the p components admit a logical ordering such that the dependence between components is related to their displacement. The test is shown to be competitive with other recently developed methods under ARMA and long-range dependence structures and to achieve superior power for heavy-tailed data. The test does not assume equality of covariance matrices between the two populations, is robust to heteroscedasticity in the component variances, and requires very little computation time, which allows its use in settings with very large p. An analysis of mitochondrial calcium concentration in mouse cardiac muscles over time and of copy number variations in a glioblastoma multiforme data set from The Cancer Genome Atlas are carried out to illustrate the test.
| S-EPMC4533933 | biostudies-literature
Project description:In spite of its urgent importance in the era of big data, testing high-dimensional parameters in generalized linear models (GLMs) in the presence of high-dimensional nuisance parameters has been largely under-studied, especially with regard to constructing powerful tests for general (and unknown) alternatives. Most existing tests are powerful only against certain alternatives and may yield incorrect Type I error rates under high-dimensional nuisance parameter situations. In this paper, we propose the adaptive interaction sum of powered score (aiSPU) test in the framework of penalized regression with a non-convex penalty, called truncated Lasso penalty (TLP), which can maintain correct Type I error rates while yielding high statistical power across a wide range of alternatives. To calculate its p-values analytically, we derive its asymptotic null distribution. Via simulations, its superior finite-sample performance is demonstrated over several representative existing methods. In addition, we apply it and other representative tests to an Alzheimer's Disease Neuroimaging Initiative (ADNI) data set, detecting possible gene-gender interactions for Alzheimer's disease. We also put R package "aispu" implementing the proposed test on GitHub.
| S-EPMC7425805 | biostudies-literature
Project description:Differential abundance analysis is a crucial task in many microbiome studies, where the central goal is to identify microbiome taxa associated with certain biological or clinical conditions. There are two different modes of microbiome differential abundance analysis: the individual-based univariate differential abundance analysis and the group-based multivariate differential abundance analysis. The univariate analysis identifies differentially abundant microbiome taxa subject to multiple correction under certain statistical error measurements such as false discovery rate, which is typically complicated by the high-dimensionality of taxa and complex correlation structure among taxa. The multivariate analysis evaluates the overall shift in the abundance of microbiome composition between two conditions, which provides useful preliminary differential information for the necessity of follow-up validation studies. In this paper, we present a novel Adaptive multivariate two-sample test for Microbiome Differential Analysis (AMDA) to examine whether the composition of a taxa-set are different between two conditions. Our simulation studies and real data applications demonstrated that the AMDA test was often more powerful than several competing methods while preserving the correct type I error rate. A free implementation of our AMDA method in R software is available at https://github.com/xyz5074/AMDA.
| S-EPMC6491633 | biostudies-literature
Project description:The purpose of this article is to propose a test for two-sample location problem in high-dimensional data. In general highdimensional case, the data dimension can be much larger than the sample size and the underlying distribution may be far from normal. Existing tests requiring explicit relationship between the data dimension and sample size or designed for multivariate normal distributions may lose power significantly and even yield type I error rates strayed from nominal levels. To overcome this issue, we propose an adaptive group p-values combination test which is robust against both high dimensionality and normality. Simulation studies show that the proposed test controls type I error rates correctly and outperforms some existing tests in most situations. An Ageing Human Brain Microarray data are used to further exemplify the method.
| S-EPMC5970252 | biostudies-literature
Project description:In this paper, we first introduce Ball Divergence, a novel measure of the difference between two probability measures in separable Banach spaces, and show that the Ball Divergence of two probability measures is zero if and only if these two probability measures are identical without any moment assumption. Using Ball Divergence, we present a metric rank test procedure to detect the equality of distribution measures underlying independent samples. It is therefore robust to outliers or heavy-tail data. We show that this multivariate two sample test statistic is consistent with the Ball Divergence, and it converges to a mixture of χ2 distributions under the null hypothesis and a normal distribution under the alternative hypothesis. Importantly, we prove its consistency against a general alternative hypothesis. Moreover, this result does not depend on the ratio of the two imbalanced sample sizes, ensuring that can be applied to imbalanced data. Numerical studies confirm that our test is superior to several existing tests in terms of Type I error and power. We conclude our paper with two applications of our method: one is for virtual screening in drug development process and the other is for genome wide expression analysis in hormone replacement therapy.
| S-EPMC6192286 | biostudies-literature
Project description:Motivated by applications in genomics, we consider in this paper global and multiple testing for the comparisons of two high-dimensional linear regression models. A procedure for testing the equality of the two regression vectors globally is proposed and shown to be particularly powerful against sparse alternatives. We then introduce a multiple testing procedure for identifying unequal coordinates while controlling the false discovery rate and false discovery proportion. Theoretical justifications are provided to guarantee the validity of the proposed tests and optimality results are established under sparsity assumptions on the regression coefficients. The proposed testing procedures are easy to implement. Numerical properties of the procedures are investigated through simulation and data analysis. The results show that the proposed tests maintain the desired error rates under the null and have good power under the alternative at moderate sample sizes. The procedures are applied to the Framingham Offspring study to investigate the interactions between smoking and cardiovascular related genetic mutations important for an inflammation marker.
| S-EPMC5788049 | biostudies-literature
Project description:Testing correlation structures has attracted extensive attention in the literature due to both its importance in real applications and several major theoretical challenges. The aim of this paper is to develop a general framework of testing correlation structures for the one-, two-, and multiple sample testing problems under a high-dimensional setting when both the sample size and data dimension go to infinity. Our test statistics are designed to deal with both the dense and sparse alternatives. We systematically investigate the asymptotic null distribution, power function, and unbiasedness of each test statistic. Theoretically, we make great efforts to deal with the non-independency of all random matrices of the sample correlation matrices. We use simulation studies and real data analysis to illustrate the versatility and practicability of our test statistics.
| S-EPMC6709985 | biostudies-literature
Project description:We develop a Bayes factor based testing procedure for comparing two population means in high dimensional settings. In 'large-p-small-n' settings, Bayes factors based on proper priors require eliciting a large and complex p×p covariance matrix, whereas Bayes factors based on Jeffrey's prior suffer the same impediment as the classical Hotelling T 2 test statistic as they involve inversion of ill-formed sample covariance matrices. To circumvent this limitation, we propose that the Bayes factor be based on lower dimensional random projections of the high dimensional data vectors. We choose the prior under the alternative to maximize the power of the test for a fixed threshold level, yielding a restricted most powerful Bayesian test (RMPBT). The final test statistic is based on the ensemble of Bayes factors corresponding to multiple replications of randomly projected data. We show that the test is unbiased and, under mild conditions, is also locally consistent. We demonstrate the efficacy of the approach through simulated and real data examples.
| S-EPMC6364997 | biostudies-literature
Project description:This paper concerns statistical inference for longitudinal data with ultrahigh dimensional covariates. We first study the problem of constructing confidence intervals and hypothesis tests for a low dimensional parameter of interest. The major challenge is how to construct a powerful test statistic in the presence of high-dimensional nuisance parameters and sophisticated within-subject correlation of longitudinal data. To deal with the challenge, we propose a new quadratic decorrelated inference function approach, which simultaneously removes the impact of nuisance parameters and incorporates the correlation to enhance the efficiency of the estimation procedure. When the parameter of interest is of fixed dimension, we prove that the proposed estimator is asymptotically normal and attains the semiparametric information bound, based on which we can construct an optimal Wald test statistic. We further extend this result and establish the limiting distribution of the estimator under the setting with the dimension of the parameter of interest growing with the sample size at a polynomial rate. Finally, we study how to control the false discovery rate (FDR) when a vector of high-dimensional regression parameters is of interest. We prove that applying the Storey (2002)'s procedure to the proposed test statistics for each regression parameter controls FDR asymptotically in longitudinal data. We conduct simulation studies to assess the finite sample performance of the proposed procedures. Our simulation results imply that the newly proposed procedure can control both Type I error for testing a low dimensional parameter of interest and the FDR in the multiple testing problem. We also apply the proposed procedure to a real data example.
| S-EPMC8277154 | biostudies-literature