## LFDR.MLE-package function | R Documentation

Suite of R functions for the estimation of the local false discovery rate (LFDR) using Type II maximum likelihood estimation (MLE):

## Inference to the best explanation of the evidence

The *p* value and Bayesian methods have well known drawbacks when it comes to measuring the strength of the evidence supporting one hypothesis over another. To overcome those drawbacks, this paper proposes an alternative method of quantifying how much support a hypothesis has from evidence consisting of data.

D. R. Bickel, “The strength of statistical evidence for composite hypotheses: Inference to the best explanation,” *Statistica Sinica* **22**, 1147-1198 (2012). Full article | 2010 version

The special law of likelihood has many advantages over more commonly used approaches to measuring the strength of statistical evidence. However, it only can measure the support of a hypothesis that corresponds to a single distribution. The proposed general law of likelihood also can measure the extent to which the data support a hypothesis that corresponds to multiple distributions. That is accomplished by formalizing inference to the best explanation.

## Uncertainty propagation for empirical Bayes interval estimates: A fiducial approach

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

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

A. Karimnezhad and D. R. Bickel, “Incorporating prior knowledge about genetic variants into the analysis of genetic association data: An empirical Bayes approach,” Working Paper, University of Ottawa, deposited in uO Research at http://hdl.handle.net/10393/34889 (2016). 2016 preprint

## Empirical Bayes single-comparison procedure

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 version | 2011 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

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 http://hdl.handle.net/10393/34295 (2016). 2016 preprint

## Empirical Bayes software (R packages)

Empirical Bayes software packages: