Archive for the ‘empirical Bayes’ Category

Uncertainty propagation for empirical Bayes interval estimates: A fiducial approach

1 December 2017 Comments off

D. R. Bickel, “Confidence distributions applied to propagating uncertainty to inference based on estimating the local false discovery rate: A fiducial continuum from confidence sets to empirical Bayes set estimates as the number of comparisons increases,” Communications in Statistics – Theory and Methods 46, 10788-10799 (2017). Published article | Free access (limited time)2014 preprint

Publication Cover

Two problems confronting the eclectic approach to statistics result from its lack of a unifying theoretical foundation. First, there is typically no continuity between a p-value reported as a level of evidence for a hypothesis in the absence of the information needed to estimate a relevant prior on one hand and an estimated posterior probability of a hypothesis reported in the presence of such information on the other hand. Second, the empirical Bayes methods recommended do not propagate the uncertainty due to estimating the prior.

The latter problem is addressed by applying a coherent form of fiducial inference to hierarchical models, yielding empirical Bayes set estimates that reflect uncertainty in estimating the prior. Plugging in the maximum likelihood estimator, while not propagating that uncertainty, provides continuity from single comparisons to large numbers of comparisons.

Estimates of the local false discovery rate based on prior information: Application to GWAS

1 August 2016 Comments off

Empirical Bayes single-comparison procedure

1 July 2016 Comments off

D. R. Bickel, “Small-scale inference: Empirical Bayes and confidence methods for as few as a single comparison,” International Statistical Review 82, 457-476 (2014). Published version2011 preprint | Simple explanation (link added 21 June 2017)

Parametric empirical Bayes methods of estimating the local false discovery rate by maximum likelihood apply not only to the large-scale settings for which they were developed, but, with a simple modification, also to small numbers of comparisons. In fact, data for a single comparison are sufficient under broad conditions, as seen from applications to measurements of the abundance levels of 20 proteins and from simulation studies with confidence-based inference as the competitor.

Adaptively selecting an empirical Bayes reference class

1 June 2016 Comments off

F. A. Aghababazadeh, M. Alvo, and D. R. Bickel, “Estimating the local false discovery rate via a bootstrap solution to the reference class problem,” Working Paper, University of Ottawa, deposited in uO Research at (2016). 2016 preprint

Categories: empirical Bayes, preprints

Empirical Bayes software (R packages)

1 May 2016 Comments off
Categories: empirical Bayes, software

False discovery rates are misleadingly low

2 March 2016 Comments off

D. R. Bickel, “Correcting false discovery rates for their bias toward false positives,” Working Paper, University of Ottawa, deposited in uO Research at (2016). 2016 preprint | Slides: CFDR and RFDR for SSC 2017

12 June 2017: URL updated and slides added


Inference after checking the prior & sampling model

1 September 2015 Comments off

D. R. Bickel, “Inference after checking multiple Bayesian models for data conflict and applications to mitigating the influence of rejected priors,” International Journal of Approximate Reasoning 66, 53–72 (2015). Simple explanation | Published version2014 preprint | Slides


The proposed procedure combines Bayesian model checking with robust Bayes acts to guide inference whether or not the model is found to be inadequate:

  1. The first stage of the procedure checks each model within a large class of models to determine which models are in conflict with the data and which are adequate for purposes of data analysis.
  2. The second stage of the procedure applies distribution combination or decision rules developed for imprecise probability.

This proposed procedure is illustrated by the application of a class of hierarchical models to a simple data set.

The link Simple explanation was added on 6 June 2017.