QVALITY: non-parametric estimation of q-values and posterior error probabilities (2009)
Käll, Lukas, Storey, John D., Noble, William Stafford
Summary: Qvality is a C++ program for estimating two types of standard statistical confidence measures: the q-value, which is an analog of the p-value that incorporates multiple testing correction,...
Biswas, Shameek, Storey, John D, Akey, Joshua M
Abstract Background The combination of gene expression profiling with linkage analysis has become a powerful paradigm for mapping gene expression quantitative trait loci (eQTL). To date, most studies...
Mapping the Genetic Architecture of Gene Expression in Human Liver (2008)
Eric E. Schadt, Cliona Molony, Eugene Chudin, Ke Hao, Xia Yang, Pek Y. Lum, ...
Genetic variants that are associated with common human diseases do not lead directly to disease, but instead act on intermediate, molecular phenotypes that in turn induce changes in higher-order...
Function digraphs of quadratic maps modulo p. Fibonacci Quart (2008)
Christie L. Gilbert, Joseph D. Kolesar, Clifford A. Reiter, John D. Storey
In this paper we will consider geometric representations of the iteration of quadratic polynomials modulo p. This is a discrete analogue of the classical quadratic Julia sets which have been the...
Optimality Driven Nearest Centroid Classification from Genomic Data (2008)
Alan R. Dabney, John D. Storey
Nearest-centroid classifiers have recently been successfully employed in high-dimensional applications, such as in genomics. A necessary step when building a classifier for high-dimensional data is...
BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btk005 Gene expression (2008)
Edge Extraction, Jeffrey T. Leek, Eva Monsen, Alan R. Dabney, John D. Storey
Summary: EDGE (Extraction of Differential Gene Expression) is an open source, point-and-click software program for the significance analysis of DNA microarray experiments. EDGE can perform both...
Idaghdour, Youssef, Storey, John D., Jadallan, Sami J., Gibson, Greg
The different environments that humans experience are likely to impact physiology and disease susceptibility. In order to estimate the magnitude of the impact of environment on transcript abundance,...
Eigen-R2 for dissecting variation in high-dimensional studies (2008)
Summary: We provide a new statistical algorithm and software package called ‘eigen-R2’ for dissecting the variation of a high-dimensional biological dataset with respect to other measured...
Harnessing naturally randomized transcription to infer regulatory relationships among genes (2007)
Chen, Lin S, Emmert-Streib, Frank, Storey, John D
Abstract We develop an approach utilizing randomized genotypes to rigorously infer causal regulatory relationships among genes at the transcriptional level, based on experiments in which genotyping...
Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis (2007)
Jeffrey T. Leek, John D. Storey
It has unambiguously been shown that genetic, environmental, demographic, and technical factors may have substantial effects on gene expression levels. In addition to the measured variable(s) of...
Capturing Heterogeneity in Gene Expression Studies by "Surrogate Variable Analysis" (2007)
Jeffrey T. Leek, John D. Storey
It has unambiguously been shown that genetic, environmental, demographic, and technical factors may have substantial effects on gene expression levels. In addition to the measured variable(s) of...
Storey, John D., Dai, James Y., Leek, Jeffrey T.
As much of the focus of genetics and molecular biology has shifted toward the systems level, it has become increasingly important to accurately extract biologically relevant signal from thousands of...
Dabney, Alan R, Storey, John D
Abstract In normalizing two-channel expression arrays, the ANOVA approach explicitly incorporates the experimental design in its model, and the MA plot-based approach accounts for intensity-dependent...
A new approach to intensity-dependent normalization of two-channel microarrays (2007)
Dabney, Alan R., Storey, John D.
A two-channel microarray measures the relative expression levels of thousands of genes from a pair of biological samples. In order to reliably compare gene expression levels between and within...
On the Structure of Multiple Testing Procedures (2006)
Leek, Jeffrey, Storey, John D.
The field of "multiple hypothesis testing" has traditionally focused on defining and estimating various error measures based on the p-values individually obtained from each test. In this paper we...
On the Structure of Multiple Testing Procedures (2006)
Leek, Jeffrey, Storey, John D.
The field of "multiple hypothesis testing" has traditionally focused on defining and estimating various error measures based on the p-values individually obtained from each test. In this paper we...
On the Structure of Multiple Testing Procedures (2006)
Leek, Jeffrey, Storey, John D.
The field of "multiple hypothesis testing" has traditionally focused on defining and estimating various error measures based on the p-values individually obtained from each test. In this paper we...
On the Structure of Multiple Testing Procedures (2006)
Leek, Jeffrey, Storey, John D.
The field of "multiple hypothesis testing" has traditionally focused on defining and estimating various error measures based on the p-values individually obtained from each test. In this paper we...
Functional ANOVA Normalization of Two-Channel Microarrays (2006)
We present a new, general method for normalizing two-channel microarray data, partially drawing on ideas from two widely used approaches. Whereas the ANOVA approach carefully distinguishes different...
Functional ANOVA Normalization of Two-Channel Microarrays (2006)
We present a new, general method for normalizing two-channel microarray data, partially drawing on ideas from two widely used approaches. Whereas the ANOVA approach carefully distinguishes different...
Functional ANOVA Normalization of Two-Channel Microarrays (2006)
We present a new, general method for normalizing two-channel microarray data, partially drawing on ideas from two widely used approaches. Whereas the ANOVA approach carefully distinguishes different...
Functional ANOVA Normalization of Two-Channel Microarrays (2006)
We present a new, general method for normalizing two-channel microarray data, partially drawing on ideas from two widely used approaches. Whereas the ANOVA approach carefully distinguishes different...
A reanalysis of a published Affymetrix GeneChip control dataset (2006)
Dabney, Alan R, Storey, John D
A response to Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset by SE Choe, M Boutros, AM Michelson, GM Church and MS Halfon. Genome Biology 2005, 6:...
EDGE: extraction and analysis of differential gene expression (2006)
Leek, Jeffrey T., Monsen, Eva, Dabney, Alan R., Storey, John D.
A New Approach to Intensity-Dependent Normalization of Two-Channel Microarrays (2006)
Dabney, Alan R., Storey, John D.
A two-channel microarray measures the relative expression levels of thousands of genes from a pair of biological samples. In order to reliably compare gene expression levels between and within...
Storey, John D., Dai, James Y., Leek, Jeffrey T.
As much of the focus of genetics and molecular biology has shifted toward the systems level, it has become increasingly important to accurately extract biologically relevant signal from thousands of...
A New Approach to Intensity-Dependent Normalization of Two-Channel Microarrays (2005)
Dabney, Alan R., Storey, John D.
A two-channel microarray measures the relative expression levels of thousands of genes from a pair of biological samples. In order to reliably compare gene expression levels between and within...
Dabney, Alan R., Storey, John D.
Nearest centroid classifiers have recently been successfully employed in high-dimensional applications. A necessary step when building a classifier for high-dimensional data is feature selection....
A New Approach to Intensity-Dependent Normalization of Two-Channel Microarrays (2005)
Dabney, Alan R., Storey, John D.
A two-channel microarray measures the relative expression levels of thousands of genes from a pair of biological samples. In order to reliably compare gene expression levels between and within...
Dabney, Alan R., Storey, John D.
Nearest centroid classifiers have recently been successfully employed in high-dimensional applications. A necessary step when building a classifier for high-dimensional data is feature selection....
A New Approach to Intensity-Dependent Normalization of Two-Channel Microarrays (2005)
Dabney, Alan R., Storey, John D.
A two-channel microarray measures the relative expression levels of thousands of genes from a pair of biological samples. In order to reliably compare gene expression levels between and within...
Dabney, Alan R., Storey, John D.
Nearest centroid classifiers have recently been successfully employed in high-dimensional applications. A necessary step when building a classifier for high-dimensional data is feature selection....
A New Approach to Intensity-Dependent Normalization of Two-Channel Microarrays (2005)
Dabney, Alan R., Storey, John D.
A two-channel microarray measures the relative expression levels of thousands of genes from a pair of biological samples. In order to reliably compare gene expression levels between and within...
Dabney, Alan R., Storey, John D.
Nearest centroid classifiers have recently been successfully employed in high-dimensional applications. A necessary step when building a classifier for high-dimensional data is feature selection....
The Optimal Discovery Procedure: A New Approach to Simultaneous Significance Testing (2005)
Significance testing is one of the main objectives of statistics. The Neyman-Pearson lemma provides a simple rule for optimally testing a single hypothesis when the null and alternative distributions...
The Optimal Discovery Procedure: A New Approach to Simultaneous Significance Testing (2005)
Significance testing is one of the main objectives of statistics. The Neyman-Pearson lemma provides a simple rule for optimally testing a single hypothesis when the null and alternative distributions...
The Optimal Discovery Procedure: A New Approach to Simultaneous Significance Testing (2005)
Significance testing is one of the main objectives of statistics. The Neyman-Pearson lemma provides a simple rule for optimally testing a single hypothesis when the null and alternative distributions...
The Optimal Discovery Procedure: A New Approach to Simultaneous Significance Testing (2005)
Significance testing is one of the main objectives of statistics. The Neyman-Pearson lemma provides a simple rule for optimally testing a single hypothesis when the null and alternative distributions...
Storey, John D., Dai, James Y., Leek, Jeffrey T.
As much of the focus of genetics and molecular biology has shifted toward the systems level, it has become increasingly important to accurately extract biologically relevant signal from thousands of...
Storey, John D., Dai, James Y., Leek, Jeffrey T.
As much of the focus of genetics and molecular biology has shifted toward the systems level, it has become increasingly important to accurately extract biologically relevant signal from thousands of...
Storey, John D., Dai, James Y., Leek, Jeffrey T.
As much of the focus of genetics and molecular biology has shifted toward the systems level, it has become increasingly important to accurately extract biologically relevant signal from thousands of...
Storey, John D., Dai, James Y., Leek, Jeffrey T.
As much of the focus of genetics and molecular biology has shifted toward the systems level, it has become increasingly important to accurately extract biologically relevant signal from thousands of...
Multiple Locus Linkage Analysis of Genomewide Expression in Yeast (2005)
John D. Storey, Joshua M. Akey, Leonid Kruglyak
Complex traits are frequently under control of multiple loci. This new method simultaneously maps multiple gene expression quantitative trait loci and assesses their significance within Saccharomyces...
Multiple Locus Linkage Analysis of Genomewide Expression in Yeast (2005)
John D. Storey, Joshua M. Akey, Leonid Kruglyak
With the ability to measure thousands of related phenotypes from a single biological sample, it is now feasible to genetically dissect systems-level biological phenomena. The genetics of...
EDGE: Extraction and Analysis of Differential Gene Expression (2005)
Leek, Jeffrey T., Monsen, Eva, Dabney, Alan R., Storey, John D.
Summary: EDGE (Extraction of Differential Gene Expression) is an open source, point-and-click software program for the significance analysis of DNA microarray experiments. EDGE can perform both...
Significance Analysis of Time Course Microarray Experiments (2004)
Storey, John D., Xiao, Wenzhong, Leek, Jeffrey T., Tompkins, Ronald G., Davis, Ron W.
Characterizing the genome-wide dynamic regulation of gene expression is important and will be of much interest in the future. However, there is currently no established method for identifying...
Significance Analysis of Time Course Microarray Experiments (2004)
Storey, John D., Xiao, Wenzhong, Leek, Jeffrey T., Tompkins, Ronald G., Davis, Ron W.
Characterizing the genome-wide dynamic regulation of gene expression is important and will be of much interest in the future. However, there is currently no established method for identifying...
Significance Analysis of Time Course Microarray Experiments (2004)
Storey, John D., Xiao, Wenzhong, Leek, Jeffrey T., Tompkins, Ronald G., Davis, Ron W.
Characterizing the genome-wide dynamic regulation of gene expression is important and will be of much interest in the future. However, there is currently no established method for identifying...
Significance Analysis of Time Course Microarray Experiments (2004)
Storey, John D., Xiao, Wenzhong, Leek, Jeffrey T., Tompkins, Ronald G., Davis, Ron W.
Characterizing the genome-wide dynamic regulation of gene expression is important and will be of much interest in the future. However, there is currently no established method for identifying...
The positive false discovery rate: a Bayesian interpretation and the q-value (2003)
Multiple hypothesis testing is concerned with controlling the rate of false positives when testing several hypotheses simultaneously. One multiple hypothesis testing error measure is the false...
Statistical significance for genome-wide experiments (2003)
John D. Storey, Robert Tibshirani
Abstract: With the increase in genome-wide experiments and the sequencing of multi-ple genomes, the analysis of large data sets has become commonplace in biology. It is often the case that thousands...
In Vivo Regulation of Human Skeletal Muscle Gene Expression by Thyroid Hormone (2002)
Karine Clément, Nathalie Viguerie, Maximilian Diehn, Ash Alizadeh, Pierre Barbe, Claire Thalamas, ...
Access the most recent version at doi: 10.1101/gr.207702
Empirical bayes methods and false discovery rates for microarrays (2002)
Bradley Efron, John D. Storey, Robert Tibshirani
In a classic two-sample problem one might use Wilcoxon's statistic to test for a dierence between Treatment and Control subjects. The analogous microarray experiment yields thousands of Wilcoxon...
In Vivo Regulation of Human Skeletal Muscle Gene Expression by Thyroid Hormone (2002)
Clément, Karine, Viguerie, Nathalie, Diehn, Maximilian, Alizadeh, Ash, Barbe, Pierre, Thalamas, Claire, ...
A manual for DNAMIX Version 2 (1998)
This document is a manual for the computer program DNAMIX v.2, which performs calculations for the formulas and methods presented in [1]. Up-to-date information on DNAMIX v.1 or DNAMIX v.2 is...
Precision and functional specificity in mRNA decay
Wang, Yulei, Liu, Chih Long, Storey, John D., Tibshirani, Robert J., Herschlag, Daniel, Brown, Patrick O.
Posttranscriptional processing of mRNA is an integral component of the gene expression program. By using DNA microarrays, we precisely measured the decay of each yeast mRNA, after thermal...
Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae
Arava, Yoav, Wang, Yulei, Storey, John D., Liu, Chih Long, Brown, Patrick O., Herschlag, Daniel
We have analyzed the translational status of each mRNA in rapidly growing Saccharomyces cerevisiae. mRNAs were separated by velocity sedimentation on a sucrose gradient, and 14 fractions across the...
Statistical significance for genomewide studies
Storey, John D., Tibshirani, Robert
With the increase in genomewide experiments and the sequencing of multiple genomes, the analysis of large data sets has become commonplace in biology. It is often the case that thousands of features...
Multiple Locus Linkage Analysis of Genomewide Expression in Yeast
Storey, John D, Akey, Joshua M, Kruglyak, Leonid
With the ability to measure thousands of related phenotypes from a single biological sample, it is now feasible to genetically dissect systems-level biological phenomena. The genetics of...
Significance analysis of time course microarray experiments
Storey, John D., Xiao, Wenzhong, Leek, Jeffrey T., Tompkins, Ronald G., Davis, Ronald W.
Characterizing the genome-wide dynamic regulation of gene expression is important and will be of much interest in the future. However, there is currently no established method for identifying...
Genetic interactions between polymorphisms that affect gene expression in yeast
Brem, Rachel B., Storey, John D., Whittle, Jacqueline, Kruglyak, Leonid
Interactions between polymorphisms at different quantitative trait loci (QTLs) are thought to contribute to the genetics of many traits, and can dramatically impact the power of genetic studies to...
In Vivo Regulation of Human Skeletal Muscle Gene Expression by Thyroid Hormone
Clément, Karine, Viguerie, Nathalie, Diehn, Maximilian, Alizadeh, Ash, Barbe, Pierre, Thalamas, Claire, ...
Thyroid hormones are key regulators of metabolism that modulate transcription via nuclear receptors. Hyperthyroidism is associated with increased metabolic rate, protein breakdown, and weight loss....
A reanalysis of a published Affymetrix GeneChip control dataset
Dabney, Alan R, Storey, John D
A response to Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset by SE Choe, M Boutros, AM Michelson, GM Church and MS Halfon. Genome Biology 2005, 6:R16
Relaxed Significance Criteria for Linkage Analysis
Linkage analysis involves performing significance tests at many loci located throughout the genome. Traditional criteria for declaring a linkage statistically significant have been formulated with...
Precision and functional specificity in mRNA decay
Wang, Yulei, Liu, Chih Long, Storey, John D., Tibshirani, Robert J., Herschlag, Daniel, Brown, Patrick O.
Posttranscriptional processing of mRNA is an integral component of the gene expression program. By using DNA microarrays, we precisely measured the decay of each yeast mRNA, after thermal...
Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae
Arava, Yoav, Wang, Yulei, Storey, John D., Liu, Chih Long, Brown, Patrick O., Herschlag, Daniel
We have analyzed the translational status of each mRNA in rapidly growing Saccharomyces cerevisiae. mRNAs were separated by velocity sedimentation on a sucrose gradient, and 14 fractions across the...
In Vivo Regulation of Human Skeletal Muscle Gene Expression by Thyroid Hormone
Clément, Karine, Viguerie, Nathalie, Diehn, Maximilian, Alizadeh, Ash, Barbe, Pierre, Thalamas, Claire, ...
Thyroid hormones are key regulators of metabolism that modulate transcription via nuclear receptors. Hyperthyroidism is associated with increased metabolic rate, protein breakdown, and weight loss....
Statistical significance for genomewide studies
Storey, John D., Tibshirani, Robert
With the increase in genomewide experiments and the sequencing of multiple genomes, the analysis of large data sets has become commonplace in biology. It is often the case that thousands of features...
Multiple Locus Linkage Analysis of Genomewide Expression in Yeast
Storey, John D, Akey, Joshua M, Kruglyak, Leonid
With the ability to measure thousands of related phenotypes from a single biological sample, it is now feasible to genetically dissect systems-level biological phenomena. The genetics of...
Significance analysis of time course microarray experiments
Storey, John D., Xiao, Wenzhong, Leek, Jeffrey T., Tompkins, Ronald G., Davis, Ronald W.
Characterizing the genome-wide dynamic regulation of gene expression is important and will be of much interest in the future. However, there is currently no established method for identifying...
A reanalysis of a published Affymetrix GeneChip control dataset
Dabney, Alan R, Storey, John D
A response to Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset by SE Choe, M Boutros, AM Michelson, GM Church and MS Halfon. Genome Biology 2005, 6:R16
Relaxed Significance Criteria for Linkage Analysis
Linkage analysis involves performing significance tests at many loci located throughout the genome. Traditional criteria for declaring a linkage statistically significant have been formulated with...
A direct approach to false discovery rates
Multiple-hypothesis testing involves guarding against much more complicated errors than single-hypothesis testing. Whereas we typically control the type I error rate for a single-hypothesis test, a...
John D. Storey, Jonathan E. Taylor, David Siegmund
The false discovery rate (FDR) is a multiple hypothesis testing quantity that describes the expected proportion of false positive results among all rejected null hypotheses. Benjamini and Hochberg...
Dabney, Alan R, Storey, John D
eCADS is a new method for multiple array normalization of two-channel microarrays that takes into account general experimental designs and intensity-dependent relationships and allows for a more...
Gene-Expression Variation Within and Among Human Populations
Storey, John D., Madeoy, Jennifer, Strout, Jeanna L., Wurfel, Mark, Ronald, James, Akey, Joshua M.
Understanding patterns of gene-expression variation within and among human populations will provide important insights into the molecular basis of phenotypic diversity and the interpretation of...
Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis
Leek, Jeffrey T, Storey, John D
It has unambiguously been shown that genetic, environmental, demographic, and technical factors may have substantial effects on gene expression levels. In addition to the measured variable(s) of...
Optimality Driven Nearest Centroid Classification from Genomic Data
Dabney, Alan R., Storey, John D.
Nearest-centroid classifiers have recently been successfully employed in high-dimensional applications, such as in genomics. A necessary step when building a classifier for high-dimensional data is...
Harnessing naturally randomized transcription to infer regulatory relationships among genes
Chen, Lin S, Emmert-Streib, Frank, Storey, John D
An approach is developed that utilizes randomized genotypes to rigorously infer causal regulatory relationships among genes at the transcriptional level. The approach is applied to an experiment in...
Idaghdour, Youssef, Storey, John D., Jadallah, Sami J., Gibson, Greg
The different environments that humans experience are likely to impact physiology and disease susceptibility. In order to estimate the magnitude of the impact of environment on transcript abundance,...
The optimal discovery procedure: a new approach to simultaneous significance testing
The Neyman-Pearson lemma provides a simple procedure for optimally testing a single hypothesis when the null and alternative distributions are known. This result has played a major role in the...
Mapping the Genetic Architecture of Gene Expression in Human Liver
Schadt, Eric E, Molony, Cliona, Chudin, Eugene, Hao, Ke, Yang, Xia, Lum, Pek Y, ...
Genetic variants that are associated with common human diseases do not lead directly to disease, but instead act on intermediate, molecular phenotypes that in turn induce changes in higher-order...
Calibrating the Performance of SNP Arrays for Whole-Genome Association Studies
Hao, Ke, Schadt, Eric E., Storey, John D.
To facilitate whole-genome association studies (WGAS), several high-density SNP genotyping arrays have been developed. Genetic coverage and statistical power are the primary benchmark metrics in...
A general framework for multiple testing dependence
Leek, Jeffrey T., Storey, John D.
We develop a general framework for performing large-scale significance testing in the presence of arbitrarily strong dependence. We derive a low-dimensional set of random vectors, called a dependence...
qvality: non-parametric estimation of q-values and posterior error probabilities
Käll, Lukas, Storey, John D., Noble, William Stafford
Summary: Qvality is a C++ program for estimating two types of standard statistical confidence measures: the q-value, which is an analog of the p-value that incorporates multiple testing correction,...
Käll, Lukas, Storey, John D., Noble, William Stafford
Motivation: A mass spectrum produced via tandem mass spectrometry can be tentatively matched to a peptide sequence via database search. Here, we address the problem of assigning a posterior error...