Empirical Bayes analysis of RNA sequencing experiments with auxiliary information

2019 ◽  
Vol 13 (4) ◽  
pp. 2452-2482 ◽  
Author(s):  
Kun Liang
2017 ◽  
Vol 10 (4) ◽  
pp. 543-556 ◽  
Author(s):  
Arnab Kumar Laha ◽  
Somak Dutta ◽  
Vivekananda Roy

2008 ◽  
Vol 24 (3) ◽  
pp. 393-408
Author(s):  
HyungJun Cho ◽  
Jaewoo Kang ◽  
Jae K. Lee

2015 ◽  
Vol 20 (4) ◽  
pp. 614-628 ◽  
Author(s):  
Jarad Niemi ◽  
Eric Mittman ◽  
Will Landau ◽  
Dan Nettleton

PLoS ONE ◽  
2009 ◽  
Vol 4 (10) ◽  
pp. e7454 ◽  
Author(s):  
Adam A. Margolin ◽  
Shao-En Ong ◽  
Monica Schenone ◽  
Robert Gould ◽  
Stuart L. Schreiber ◽  
...  

2001 ◽  
Vol 96 (456) ◽  
pp. 1151-1160 ◽  
Author(s):  
Bradley Efron ◽  
Robert Tibshirani ◽  
John D Storey ◽  
Virginia Tusher

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Yajie Zou ◽  
Xinzhi Zhong ◽  
John Ash ◽  
Ziqiang Zeng ◽  
Yinhai Wang ◽  
...  

Hotspot identification (HSID) is a critical part of network-wide safety evaluations. Typical methods for ranking sites are often rooted in using the Empirical Bayes (EB) method to estimate safety from both observed crash records and predicted crash frequency based on similar sites. The performance of the EB method is highly related to the selection of a reference group of sites (i.e., roadway segments or intersections) similar to the target site from which safety performance functions (SPF) used to predict crash frequency will be developed. As crash data often contain underlying heterogeneity that, in essence, can make them appear to be generated from distinct subpopulations, methods are needed to select similar sites in a principled manner. To overcome this possible heterogeneity problem, EB-based HSID methods that use common clustering methodologies (e.g., mixture models, K-means, and hierarchical clustering) to select “similar” sites for building SPFs are developed. Performance of the clustering-based EB methods is then compared using real crash data. Here, HSID results, when computed on Texas undivided rural highway cash data, suggest that all three clustering-based EB analysis methods are preferred over the conventional statistical methods. Thus, properly classifying the road segments for heterogeneous crash data can further improve HSID accuracy.


F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1408 ◽  
Author(s):  
Charity W. Law ◽  
Monther Alhamdoosh ◽  
Shian Su ◽  
Gordon K. Smyth ◽  
Matthew E. Ritchie

The ability to easily and efficiently analyse RNA-sequencing data is a key strength of the Bioconductor project. Starting with counts summarised at the gene-level, a typical analysis involves pre-processing, exploratory data analysis, differential expression testing and pathway analysis with the results obtained informing future experiments and validation studies. In this workflow article, we analyse RNA-sequencing data from the mouse mammary gland, demonstrating use of the popular edgeR package to import, organise, filter and normalise the data, followed by the limma package with its voom method, linear modelling and empirical Bayes moderation to assess differential expression and perform gene set testing. This pipeline is further enhanced by the Glimma package which enables interactive exploration of the results so that individual samples and genes can be examined by the user. The complete analysis offered by these three packages highlights the ease with which researchers can turn the raw counts from an RNA-sequencing experiment into biological insights using Bioconductor.


2018 ◽  
Vol 12 (2) ◽  
pp. 3953-4001 ◽  
Author(s):  
Ismaël Castillo ◽  
Romain Mismer

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