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Register a new userFalse Discovery Rate Computation: Illustrations and Modifications
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Added by
Megan Murray
Publication date
2020
fields
Mathematical Statistics
and research's language is
English
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False discovery rates (FDR) are an essential component of statistical inference, representing the propensity for an observed result to be mistaken. FDR estimates should accompany observed results to help the user contextualize the relevance and potential impact of findings. This paper introduces a new user-friendly R package for computing FDRs and adjusting p-values for FDR control. These tools respect the critical difference between the adjusted p-value and the estimated FDR for a particular finding, which are sometimes numerically identical but are often confused in practice. Newly augmented methods for estimating the null proportion of findings - an important part of the FDR estimation procedure - are proposed and evaluated. The package is broad, encompassing a variety of methods for FDR estimation and FDR control, and includes plotting functions for easy display of results. Through extensive illustrations, we strongly encourage wider reporting of false discovery rates for observed findings.
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Selecting relevant features associated with a given response variable is an important issue in many scientific fields. Quantifying quality and uncertainty of a selection result via false discovery rate (FDR) control has been of recent interest. This paper introduces a way of using data-splitting strategies to asymptotically control the FDR while maintaining a high power. For each feature, the method constructs a test statistic by estimating two independent regression coefficients via data splitting. FDR control is achieved by taking advantage of the statistics property that, for any null feature, its sampling distribution is symmetric about zero. Furthermore, we propose Multiple Data Splitting (MDS) to stabilize the selection result and boost the power. Interestingly and surprisingly, with the FDR still under control, MDS not only helps overcome the power loss caused by sample splitting, but also results in a lower variance of the false discovery proportion (FDP) compared with all other methods in consideration. We prove that the proposed data-splitting methods can asymptotically control the FDR at any designated level for linear and Gaussian graphical models in both low and high dimensions. Through intensive simulation studies and a real-data application, we show that the proposed methods are robust to the unknown distribution of features, easy to implement and computationally efficient, and are often the most powerful ones amongst competitors especially when the signals are weak and the correlations or partial correlations are high among features.
Variable selection on the large-scale networks has been extensively studied in the literature. While most of the existing methods are limited to the local functionals especially the graph edges, this paper focuses on selecting the discrete hub structures of the networks. Specifically, we propose an inferential method, called StarTrek filter, to select the hub nodes with degrees larger than a certain thresholding level in the high dimensional graphical models and control the false discovery rate (FDR). Discovering hub nodes in the networks is challenging: there is no straightforward statistic for testing the degree of a node due to the combinatorial structures; complicated dependence in the multiple testing problem is hard to characterize and control. In methodology, the StarTrek filter overcomes this by constructing p-values based on the maximum test statistics via the Gaussian multiplier bootstrap. In theory, we show that the StarTrek filter can control the FDR by providing accurate bounds on the approximation errors of the quantile estimation and addressing the dependence structures among the maximal statistics. To this end, we establish novel Cramer-type comparison bounds for the high dimensional Gaussian random vectors. Comparing to the Gaussian comparison bound via the Kolmogorov distance established by citet{chernozhukov2014anti}, our Cramer-type comparison bounds establish the relative difference between the distribution functions of two high dimensional Gaussian random vectors. We illustrate the validity of the StarTrek filter in a series of numerical experiments and apply it to the genotype-tissue expression dataset to discover central regulator genes.
Consider the online testing of a stream of hypotheses where a real--time decision must be made before the next data point arrives. The error rate is required to be controlled at {all} decision points. Conventional emph{simultaneous testing rules} are no longer applicable due to the more stringent error constraints and absence of future data. Moreover, the online decision--making process may come to a halt when the total error budget, or alpha--wealth, is exhausted. This work develops a new class of structure--adaptive sequential testing (SAST) rules for online false discover rate (FDR) control. A key element in our proposal is a new alpha--investment algorithm that precisely characterizes the gains and losses in sequential decision making. SAST captures time varying structures of the data stream, learns the optimal threshold adaptively in an ongoing manner and optimizes the alpha-wealth allocation across different time periods. We present theory and numerical results to show that the proposed method is valid for online FDR control and achieves substantial power gain over existing online testing rules.
Scientific hypotheses in a variety of applications have domain-specific structures, such as the tree structure of the International Classification of Diseases (ICD), the directed acyclic graph structure of the Gene Ontology (GO), or the spatial structure in genome-wide association studies. In the context of multiple testing, the resulting relationships among hypotheses can create redundancies among rejections that hinder interpretability. This leads to the practice of filtering rejection sets obtained from multiple testing procedures, which may in turn invalidate their inferential guarantees. We propose Focused BH, a simple, flexible, and principled methodology to adjust for the application of any pre-specified filter. We prove that Focused BH controls the false discovery rate under various conditions, including when the filter satisfies an intuitive monotonicity property and the p-values are positively dependent. We demonstrate in simulations that Focused BH performs well across a variety of settings, and illustrate this methods practical utility via analyses of real datasets based on ICD and GO.
We develop a new class of distribution--free multiple testing rules for false discovery rate (FDR) control under general dependence. A key element in our proposal is a symmetrized data aggregation (SDA) approach to incorporating the dependence structure via sample splitting, data screening and information pooling. The proposed SDA filter first constructs a sequence of ranking statistics that fulfill global symmetry properties, and then chooses a data--driven threshold along the ranking to control the FDR. The SDA filter substantially outperforms the knockoff method in power under moderate to strong dependence, and is more robust than existing methods based on asymptotic $p$-values. We first develop finite--sample theory to provide an upper bound for the actual FDR under general dependence, and then establish the asymptotic validity of SDA for both the FDR and false discovery proportion (FDP) control under mild regularity conditions. The procedure is implemented in the R package texttt{SDA}. Numerical results confirm the effectiveness and robustness of SDA in FDR control and show that it achieves substantial power gain over existing methods in many settings.
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