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Accounting for Dependence in Similarity Data from DNA Fingerprinting

Hepworth, Graham; Gordon, Ian; McCullough, Michael - In: Statistical Applications in Genetics and Molecular Biology 6 (2007) 1, pp. 1-1

Differentiating strains of a pathogen is often central to investigating its epidemiological aspects. The genetic similarity of a group of strains can be assessed by calculating a matrix of dissimilarities from their DNA fingerprinting profiles. The mean dissimilarity for each strain across other...

Persistent link: https://www.econbiz.de/10005459164

Population Structure and Covariate Analysis Based on Pairwise Microsatellite Allele Matching Frequencies

Givens, Geof; Ozaksoy, Isin - In: Statistical Applications in Genetics and Molecular Biology 6 (2007) 1, pp. 31-31

We describe a general model for pairwise microsatellite allele matching probabilities. The model can be used for analysis of population substructure, and is particularly focused on relating genetic correlation to measurable covariates. The approach is intended for cases when the existence of...

Persistent link: https://www.econbiz.de/10005585073

Reverse Engineering Galactose Regulation in Yeast through Model Selection

Thorsson, Vesteinn; Hörnquist, Michael; Siegel, Andrew; … - In: Statistical Applications in Genetics and Molecular Biology 4 (2007) 1, pp. 28-28

maximization of log-likelihood with Cp, AIC, and BIC penalties, bootstrap and cross-validation error estimation, and coefficient …

Persistent link: https://www.econbiz.de/10005459170

Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates

Dudoit, Sandrine; Laan, Mark van der; Pollard, Katherine - In: Statistical Applications in Genetics and Molecular Biology 3 (2009) 1, pp. 13-13

error rate. A general bootstrap algorithm is supplied to conveniently obtain consistent estimators of the null distribution … among the rejected hypotheses (van der Laan et al., 2004a). The proposed bootstrap multiple testing procedures are evaluated …

Persistent link: https://www.econbiz.de/10005046568

Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate

Laan, Mark van der; Dudoit, Sandrine; Pollard, Katherine - In: Statistical Applications in Genetics and Molecular Biology 3 (2009) 1, pp. 14-14

error rate. A general bootstrap algorithm is supplied to conveniently obtain consistent estimators of the null distribution. …

Persistent link: https://www.econbiz.de/10005046575

Quantile-Function Based Null Distribution in Resampling Based Multiple Testing

Laan, Mark van der; Hubbard, Alan - In: Statistical Applications in Genetics and Molecular Biology 5 (2009) 1, pp. 14-14

generally asymptotically valid null distribution for the test-statistics and a corresponding bootstrap estimate, whose marginal …

Persistent link: https://www.econbiz.de/10005046579

A Comparison of Methods to Control Type I Errors in Microarray Studies

Chen, Jinsong; Laan, Mark van der; Smith, Martyn; … - In: Statistical Applications in Genetics and Molecular Biology 6 (2009) 1, pp. 28-28

resampling based methods, such as permutation methods, the null-centered and scaled bootstrap (NCSB) method, and the quantile-transformed-bootstrap … suffer from that limitation, but an impractical number of bootstrap samples are often needed to get proper control of Type I …

Persistent link: https://www.econbiz.de/10005046600

Multiple Testing and Data Adaptive Regression: An Application to HIV-1 Sequence Data.

Birkner, Merrill; Sinisi, Sandra; Laan, Mark van der - In: Statistical Applications in Genetics and Molecular Biology 4 (2009) 1, pp. 8-8

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...

Persistent link: https://www.econbiz.de/10005046606

Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates

Dudoit, Sandrine; Laan, Mark van der; Pollard, Katherine - In: Statistical Applications in Genetics and Molecular Biology 3 (2007) 1, pp. 13-13

Persistent link: https://www.econbiz.de/10005752549

Adaptive Choice of the Number of Bootstrap Samples in Large Scale Multiple Testing

Guo, Wenge; Peddada, Shyamal - In: Statistical Applications in Genetics and Molecular Biology 7 (2008) 1, pp. 13-13

It is a common practice to use resampling methods such as the bootstrap for calculating the p-value for each test when … performing large scale multiple testing. The precision of the bootstrap p-values and that of the false discovery rate (FDR … important need, we developed a simple adaptive bootstrap methodology for large scale multiple testing, which reduces the total …

Persistent link: https://www.econbiz.de/10005246469