scholarly journals An empirical Bayes approach to inferring large-scale gene association networks

2004 ◽  
Vol 21 (6) ◽  
pp. 754-764 ◽  
Author(s):  
J. Schafer ◽  
K. Strimmer
Keyword(s):  
Empirical Bayes ◽  
Large Scale ◽  
Gene Association ◽  
Empirical Bayes Approach ◽  
Bayes Approach

scholarly journals An Empirical Bayes approach for the identification of long-range chromosomal interaction from Hi-C data

2021 ◽  
Vol 20 (1) ◽  
pp. 1-15
Author(s):  
Qi Zhang ◽  
Zheng Xu ◽  
Yutong Lai
Keyword(s):  
Long Range ◽  
Latent Variables ◽  
Empirical Bayes ◽  
Genome Structure ◽  
Peak Detection ◽  
Data Matrix ◽  
Dispersion Modeling ◽  
Empirical Bayes Approach ◽  
Over Dispersion ◽  
Bayes Approach

Abstract Hi-C experiments have become very popular for studying the 3D genome structure in recent years. Identification of long-range chromosomal interaction, i.e., peak detection, is crucial for Hi-C data analysis. But it remains a challenging task due to the inherent high dimensionality, sparsity and the over-dispersion of the Hi-C count data matrix. We propose EBHiC, an empirical Bayes approach for peak detection from Hi-C data. The proposed framework provides flexible over-dispersion modeling by explicitly including the “true” interaction intensities as latent variables. To implement the proposed peak identification method (via the empirical Bayes test), we estimate the overall distributions of the observed counts semiparametrically using a Smoothed Expectation Maximization algorithm, and the empirical null based on the zero assumption. We conducted extensive simulations to validate and evaluate the performance of our proposed approach and applied it to real datasets. Our results suggest that EBHiC can identify better peaks in terms of accuracy, biological interpretability, and the consistency across biological replicates. The source code is available on Github (https://github.com/QiZhangStat/EBHiC).

An empirical bayes approach to monitoring water quality

1995 ◽  
Vol 6 (1) ◽  
pp. 1-5 ◽  
Author(s):  
Andrew R. Solow ◽  
Arthur G. Gaines
Keyword(s):  
Water Quality ◽  
Empirical Bayes ◽  
Empirical Bayes Approach ◽  
Bayes Approach
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