Estimating the proportion of true null hypotheses, with application to DNA microarray data
TLDR
In this paper, the problem of estimating the proportion of true null hypotheses, π0, i n a multiple-hypothesis set-up, is considered and the tests are based on observed p-values.Abstract:
Summary. We consider the problem of estimating the proportion of true null hypotheses, π0 ,i n a multiple-hypothesis set-up. The tests are based on observed p-values. We first review published estimators based on the estimator that was suggested by Schweder and Spjotvoll. Then we derive new estimators based on nonparametric maximum likelihood estimation of the p-value density, restricting to decreasing and convex decreasing densities. The estimators of π0 are all derived under the assumption of independent test statistics. Their performance under dependence is investigated in a simulation study. We find that the estimators are relatively robust with respect to the assumption of independence and work well also for test statistics with moderate dependence.read more
Citations
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References
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Journal ArticleDOI
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Yoav Benjamini,Yosef Hochberg +1 more
TL;DR: In this paper, a different approach to problems of multiple significance testing is presented, which calls for controlling the expected proportion of falsely rejected hypotheses -the false discovery rate, which is equivalent to the FWER when all hypotheses are true but is smaller otherwise.
Book
An introduction to the bootstrap
Bradley Efron,Robert Tibshirani +1 more
TL;DR: This article presents bootstrap methods for estimation, using simple arguments, with Minitab macros for implementing these methods, as well as some examples of how these methods could be used for estimation purposes.
BookDOI
Density estimation for statistics and data analysis
TL;DR: The Kernel Method for Multivariate Data: Three Important Methods and Density Estimation in Action.
Journal ArticleDOI
Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
TL;DR: The hierarchical model of Lonnstedt and Speed (2002) is developed into a practical approach for general microarray experiments with arbitrary numbers of treatments and RNA samples and the moderated t-statistic is shown to follow a t-distribution with augmented degrees of freedom.
Journal ArticleDOI
R: A Language for Data Analysis and Graphics
Ross Ihaka,Robert Gentleman +1 more
TL;DR: In this article, the authors discuss their experience designing and implementing a statistical computing language, which combines what they felt were useful features from two existing computer languages, and they feel that the new language provides advantages in the areas of portability, computational efficiency, memory management, and scope.
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