Statistics and Probability Commons^™

Characterizing The Statistical Properties And Global Distribution Of Dansgaard-Oeschger Events, Andrea Michelle Thomas

Theses and Dissertations

Ice core records from Greenland have shown times of rapid warming during the most recent glacial period, called Dansgaard-Oeschger (D-O) events. D-O events are important to our understanding of both past climate systems and modern climate volatility. In this paper, we present new approaches for statistically evaluating the existence of cyclicity in D-O events and the possible lagged correlation between the Greenland and Antarctica temperature records. Specifically, we consider permutation testing and bootstrapping methodologies for assessing the cyclicity of D-O events and the correlation between the Greenland and Antarctica records. We find that there is not enough evidence to conclude …

Constructing Confidence Intervals For Spearman’S Rank Correlation With Ordinal Data: A Simulation Study Comparing Analytic And Bootstrap Methods, John Ruscio

Journal of Modern Applied Statistical Methods

Research shows good probability coverage using analytic confidence intervals (CIs) for Spearman’s rho with continuous data, but poorer coverage with ordinal data. A simulation study examining the latter case replicated prior results and revealed that coverage of bootstrap CIs was usually as good or better than coverage of analytic CIs.

Assessing Multivariate Heritability Through Nonparametric Methods, Benjamin Alan Carper

Theses and Dissertations

The similarities between generations of living subjects are often quantified by heritability. By distinguishing genotypic variation, or variation due to parental pairings, from phenotypic variation, or normal intraspecies variation, the heritability of traits can be estimated. Due to the multivariate nature of many traits, such as size and shape, computation of heritability can be difficult. Also, assessment of the variation of the heritability estimate is extremely difficult. This study uses nonparametric methods, namely the randomization test and the bootstrap, to obtain both a measure of the extremity of the observed heritability and an assessment of the uncertainty.

A Simple Method For Finding Emperical Liklihood Type Intervals For The Roc Curve, Ayman Baklizi

Journal of Modern Applied Statistical Methods

Interval estimation of the ROC curve is considered using the empirical likelihood techniques. Suggested is a procedure that is very simple computationally and avoids the constrained optimization problems usually faced with empirical likelihood methods. Various modifications are suggested and the performance of the intervals is evaluated in terms of their coverage probability. The results show that some of the suggested intervals compete well with other intervals known in the literature.

Beta-Weibull Distribution: Some Properties And Applications To Censored Data, Carl Lee, Felix Famoye, Olugbenga Olumolade

Journal of Modern Applied Statistical Methods

Some properties of a four-parameter beta-Weibull distribution are discussed. The beta-Weibull distribution is shown to have bathtub, unimodal, increasing, and decreasing hazard functions. The distribution is applied to censored data sets on bus-motor failures and a censored data set on head-and-neck-cancer clinical trial. A simulation is conducted to compare the beta-Weibull distribution with the exponentiated Weibull distribution.

A Method For Finding Standard Error Estimates For Rma Expression Levels Using Bootstrap, Gabriel Nicholas

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

Oligonucleotide arrays are used in many applications. Affymetrix GeneChip arrays are widely used. Before researchers can use the information from these arrays, the raw data must be transformed and summarized into a more meaningful and usable form. One of the more popular methods for doing so is RMA (Robust Multi-array Analysis).

A problem with RMA is that the end result (estimated gene expression levels) is based on a fairly complicated process that is unusual. Specifically, there is no closed-form estimate of standard errors for the estimated gene expression levels. The current recommendation is to use a naive estimate for the …

Comparing The Statistical Tests For Homogeneity Of Variances., Zhiqiang Mu

Electronic Theses and Dissertations

Testing the homogeneity of variances is an important problem in many applications since statistical methods of frequent use, such as ANOVA, assume equal variances for two or more groups of data. However, testing the equality of variances is a difficult problem due to the fact that many of the tests are not robust against non-normality. It is known that the kurtosis of the distribution of the source data can affect the performance of the tests for variance. We review the classical tests and their latest, more robust modifications, some other tests that have recently appeared in the literature, and use …

Empirical Likelihood Inference For The Area Under The Roc Curve, Gengsheng Qin, Xiao-Hua Zhou

UW Biostatistics Working Paper Series

For a continuous-scale diagnostic test, the most commonly used summary index of the receiver operating characteristic (ROC) curve is the area under the curve (AUC) that measures the accuracy of the diagnostic test. In this paper we propose an empirical likelihood approach for the inference of AUC. We first define an empirical likelihood ratio for AUC and show that its limiting distribution is a scaled chi-square distribution. We then obtain an empirical likelihood based confidence interval for AUC using the scaled chi-square distribution. This empirical likelihood inference for AUC can be extended to stratified samples and the resulting limiting distribution …

Large Sample And Bootstrap Intervals For The Gamma Scale Parameter Based On Grouped Data, Ayman Baklizi, Amjad Al-Nasser

Journal of Modern Applied Statistical Methods

Interval estimation of the scale parameter of the gamma distribution using grouped data is considered in this article. Exact intervals do not exist and approximate intervals are needed Recently, Chen and Mi (2001) proposed alternative approximate intervals. In this article, some bootstrap and jackknife type intervals are proposed. The performance of these intervals is investigated and compared. The results show that some of the suggested intervals have a satisfactory statistical performance in situations where the sample size is small with heavy proportion of censoring.

Second-Order Accurate Inference On Simple, Partial, And Multiple Correlations, Robert J. Boik, Ben Haaland

Journal of Modern Applied Statistical Methods

This article develops confidence interval procedures for functions of simple, partial, and squared multiple correlation coefficients. It is assumed that the observed multivariate data represent a random sample from a distribution that possesses infinite moments, but there is no requirement that the distribution be normal. The coverage error of conventional one-sided large sample intervals decreases at rate 1√n as n increases, where n is an index of sample size. The coverage error of the proposed intervals decreases at rate 1/n as n increases. The results of a simulation study that evaluates the performance of the proposed intervals is …

Test Statistics Null Distributions In Multiple Testing: Simulation Studies And Applications To Genomics, Katherine S. Pollard, Merrill D. Birkner, Mark J. Van Der Laan, Sandrine Dudoit

U.C. Berkeley Division of Biostatistics Working Paper Series

Multiple hypothesis testing problems arise frequently in biomedical and genomic research, for instance, when identifying differentially expressed or co-expressed genes in microarray experiments. We have developed generally applicable resampling-based single-step and stepwise multiple testing procedures (MTP) for control of a broad class of Type I error rates, defined as tail probabilities and expected values for arbitrary functions of the numbers of false positives and rejected hypotheses (Dudoit and van der Laan, 2005; Dudoit et al., 2004a,b; Pollard and van der Laan, 2004; van der Laan et al., 2005, 2004a,b). As argued in the early article of Pollard and van der …

Two Sides Of The Same Coin: Bootstrapping The Restricted Vs. Unrestricted Model, Panagiotis Mantalos

Journal of Modern Applied Statistical Methods

The properties of the bootstrap test for restrictions are studied in two versions: 1) bootstrapping under the null hypothesis, restricted, and 2) bootstrapping under the alternative hypothesis, unrestricted. This article demonstrates the equivalence of these two methods, and illustrates the small sample properties of the Wald test for testing Granger-Causality in a stable stationary VAR system by Monte Carlo methods. The analysis regarding the size of the test reveals that, as expected, both bootstrap tests have actual sizes that lie close to the nominal size. Regarding the power of the test, the Wald and bootstrap tests share the same power …

Testing The Goodness Of Fit Of Multivariate Multiplicative-Intercept Risk Models Based On Case-Control Data, Biao Zhang

Journal of Modern Applied Statistical Methods

The validity of the multivariate multiplicative-intercept risk model with I +1 categories based on casecontrol data is tested. After reparametrization, the assumed risk model is equivalent to an (I +1) -sample semiparametric model in which the I ratios of two unspecified density functions have known parametric forms. By identifying this (I +1) -sample semiparametric model, which is of intrinsic interest in general (I +1) -sample problems, with an (I +1) -sample semiparametric selection bias model, we propose a weighted Kolmogorov-Smirnov-type statistic to test the validity of the multivariate multiplicativeintercept risk model. Established are some asymptotic results …

New Confidence Intervals For The Difference Between Two Sensitivities At A Fixed Level Of Specificity, Gengsheng Qin, Yu-Sheng Hsu, Xiao-Hua Zhou

UW Biostatistics Working Paper Series

For two continuous-scale diagnostic tests, it is of interest to compare their sensitivities at a predetermined level of specificity. In this paper we propose three new intervals for the difference between two sensitivities at a fixed level of specificity. These intervals are easy to compute. We also conduct simulation studies to compare the relative performance of the new intervals with the existing normal approximation based interval proposed by Wieand et al (1989). Our simulation results show that the newly proposed intervals perform better than the existing normal approximation based interval in terms of coverage accuracy and interval length.

Cluster Analysis Of Genomic Data With Applications In R, Katherine S. Pollard, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

In this paper, we provide an overview of existing partitioning and hierarchical clustering algorithms in R. We discuss statistical issues and methods in choosing the number of clusters, the choice of clustering algorithm, and the choice of dissimilarity matrix. In particular, we illustrate how the bootstrap can be employed as a statistical method in cluster analysis to establish the reproducibility of the clusters and the overall variability of the followed procedure. We also show how to visualize a clustering result by plotting ordered dissimilarity matrices in R. We present a new R package, hopach, which implements the hybrid clustering method, …

Multiple Testing Procedures And Applications To Genomics, Merrill D. Birkner, Katherine S. Pollard, Mark J. Van Der Laan, Sandrine Dudoit

U.C. Berkeley Division of Biostatistics Working Paper Series

This chapter proposes widely applicable resampling-based single-step and stepwise multiple testing procedures (MTP) for controlling a broad class of Type I error rates, in testing problems involving general data generating distributions (with arbitrary dependence structures among variables), null hypotheses, and test statistics (Dudoit and van der Laan, 2005; Dudoit et al., 2004a,b; van der Laan et al., 2004a,b; Pollard and van der Laan, 2004; Pollard et al., 2005). Procedures are provided to control Type I error rates defined as tail probabilities for arbitrary functions of the numbers of Type I errors, V_n, and rejected hypotheses, R_n. These error rates include: …

Multiple Testing Procedures For Controlling Tail Probability Error Rates, Sandrine Dudoit, Mark J. Van Der Laan, Merrill D. Birkner

U.C. Berkeley Division of Biostatistics Working Paper Series

The present article discusses and compares multiple testing procedures (MTP) for controlling Type I error rates defined as tail probabilities for the number (gFWER) and proportion (TPPFP) of false positives among the rejected hypotheses. Specifically, we consider the gFWER- and TPPFP-controlling MTPs proposed recently by Lehmann & Romano (2004) and in a series of four articles by Dudoit et al. (2004), van der Laan et al. (2004b,a), and Pollard & van der Laan (2004). The former Lehmann & Romano (2004) procedures are marginal, in the sense that they are based solely on the marginal distributions of the test statistics, i.e., …

Multiple Testing Procedures: R Multtest Package And Applications To Genomics, Katherine S. Pollard, Sandrine Dudoit, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

The Bioconductor R package multtest implements widely applicable resampling-based single-step and stepwise multiple testing procedures (MTP) for controlling a broad class of Type I error rates, in testing problems involving general data generating distributions (with arbitrary dependence structures among variables), null hypotheses, and test statistics. The current version of multtest provides MTPs for tests concerning means, differences in means, and regression parameters in linear and Cox proportional hazards models. Procedures are provided to control Type I error rates defined as tail probabilities for arbitrary functions of the numbers of false positives and rejected hypotheses. These error rates include tail probabilities …

Size And Power Of The Reset Test As Applied To Systems Of Equations: A Bootstrap Approach, Ghazi Shukur, Panagiotis Mantalos

Journal of Modern Applied Statistical Methods

The size and power of various generalization of the RESET test for functional misspecification are investigated, using the “Bootsrap critical values”, in systems ranging from one to ten equations. The properties of 8 versions of the test are studied using Monte Carlo methods. The results are then compared with another study of Shukur and Edgerton (2002), in which they used the asymptotic critical values instead and found that in general only one version of the tests works well regarding size properties. In our study, when applying the bootstrap critical values, we find that all the tests exhibits correct size even …

Interval Estimation For The Scale Parameter Of Burr Type X Distribution Based On Grouped Data, Amjad D. Al-Nasser, Ayman Baklizi

Journal of Modern Applied Statistical Methods

The application of some bootstrap type intervals for the scale parameter of the Burr type X distribution with grouped data is proposed. The general asymptotic confidence interval procedure (Chen & Mi, 2001) is studied. The performance of these intervals is investigated and compared. Some of the bootstrap intervals give better performance for situations of small sample size and heavy censoring.

Multiple Testing And Data Adaptive Regression: An Application To Hiv-1 Sequence Data, Merrill D. Birkner, Sandra E. Sinisi, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

Analysis of viral strand sequence data and viral replication capacity could potentially lead to biological insights regarding the replication ability of HIV-1. Determining specific target codons on the viral strand will facilitate the manufacturing of target specific antiretrovirals. Various algorithmic and analysis techniques can be applied to this application. We propose using multiple testing to find codons which have significant univariate associations with replication capacity of the virus. We also propose using a data adaptive multiple regression algorithm to obtain multiple predictions of viral replication capacity based on an entire mutant/non-mutant sequence profile. The data set to which these techniques …

Nonparametric Confidence Intervals For The One- And Two-Sample Problems, Xiao-Hua Zhou, Phillip Dinh

UW Biostatistics Working Paper Series

Confidence intervals for the mean of one sample and the difference in means of two independent samples based on the ordinary-t statistic suffer deficiencies when samples come from skewed distributions. In this article, we evaluate several existing techniques and propose new methods to improve coverage accuracy. The methods examined include the ordinary-t, the bootstrap-t, the biased-corrected acceleration (BCa) bootstrap, and three new intervals based on transformation of the t-statistic. Our study shows that our new transformation intervals and the bootstrap-t intervals give best coverage accuracy for a variety of skewed distributions; and that our new transformation intervals have shorter interval …

Multiple Testing. Part Ii. Step-Down Procedures For Control Of The Family-Wise Error Rate, Mark J. Van Der Laan, Sandrine Dudoit, Katherine S. Pollard

U.C. Berkeley Division of Biostatistics Working Paper Series

The present article proposes two step-down multiple testing procedures for asymptotic control of the family-wise error rate (FWER): the first procedure is based on maxima of test statistics (step-down maxT), while the second relies on minima of unadjusted p-values (step-down minP). A key feature of our approach is the test statistics null distribution (rather than data generating null distribution) used to derive cut-offs (i.e., rejection regions) for these test statistics and the resulting adjusted p-values. For general null hypotheses, corresponding to submodels for the data generating distribution, we identify an asymptotic domination condition for a null distribution under which the …

Confidence Intervals For P(X Less Than Y) In The Exponential Case With Common Location Parameter, Ayman Baklizi

Journal of Modern Applied Statistical Methods

The problem considered is interval estimation of the stress - strength reliability R = P(Xθ and λ respectively and a common location parameter μ . Several types of asymptotic, approximate and bootstrap intervals are investigated. Performances are investigated using simulation techniques and compared in terms of attainment of the nominal confidence level, symmetry of lower and upper error rates, and expected length. Recommendations concerning their usage are given.

Resampling-Based Multiple Testing: Asymptotic Control Of Type I Error And Applications To Gene Expression Data, Katherine S. Pollard, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

We define a general statistical framework for multiple hypothesis testing and show that the correct null distribution for the test statistics is obtained by projecting the true distribution of the test statistics onto the space of mean zero distributions. For common choices of test statistics (based on an asymptotically linear parameter estimator), this distribution is asymptotically multivariate normal with mean zero and the covariance of the vector influence curve for the parameter estimator. This test statistic null distribution can be estimated by applying the non-parametric or parametric bootstrap to correctly centered test statistics. We prove that this bootstrap estimated null …

Power Analyses When Comparing Trimmed Means, Rand R. Wilcox, H. J. Keselman

Journal of Modern Applied Statistical Methods

Given a random sample from each of two independent groups, this article takes up the problem of estimating power, as well as a power curve, when comparing 20% trimmed means with a percentile bootstrap method. Many methods were considered, but only one was found to be satisfactory in terms of obtaining both a point estimate of power as well as a (one-sided) confidence interval. The method is illustrated with data from a reading study where theory suggests two groups should differ but nonsignificant results were obtained.

Statistical Inference For Simultaneous Clustering Of Gene Expression Data, Katherine S. Pollard, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

Current methods for analysis of gene expression data are mostly based on clustering and classification of either genes or samples. We offer support for the idea that more complex patterns can be identified in the data if genes and samples are considered simultaneously. We formalize the approach and propose a statistical framework for two-way clustering. A simultaneous clustering parameter is defined as a function of the true data generating distribution, and an estimate is obtained by applying this function to the empirical distribution. We illustrate that a wide range of clustering procedures, including generalized hierarchical methods, can be defined as …

Comparison Of Bootstrap With Other Tests For Several Distributions, Yu-Yu Wong

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This paper discusses results of a computer simulation to investigate several different tests when sampling several distributions. The hypothesis H₀: μ=0 was tested against H₀: μ≠0, using the usual t-test, trimmed t-test, the Jackkinfe, the Bootstrap and signed-rank test. The p-values and empirical power show that the Bootstrap is as good as the t-test. The Jackknife procedure is too liberal, always obtaining small p-values. The signed-rank is a fairly good test if the data follows the Cauchy Distribution.

Comparison Of Bootstrap And Jacknife Statistical Procedures, Amanuel Gobena

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

This report compares the bootstrapping to jacknifing statistical procedures in terms in bias, confidence interval and estimation of median. Related literature have been reviewed. A bootstrap allows a researcher to get an approximation to the distribution of possibly complicated statistical summaries. It is based on random sampling with replacement from experimental units. Jacknife has also been in operation prior to bootstrapping statistical procedure. The jacknife divides the data into subgroups and obtains partial estimates of these subgroups by omitting one subgroup at a time. When both of these statistical resampling procedures are compared the bootstrap has less bias, more accurate …