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Archive for the ‘trainee author’ Category

R functions for combining probabilities using game theory

15 November 2018 Leave a comment

Suite of R functions for combination of probabilities using a game-theoretic method

Source: Combine package | R Documentation

R package for estimating local false discovery rates using empirical Bayes methods

15 October 2018 Leave a comment

Coherent fiducial distributions

20 August 2013 Leave a comment

D. R. Bickel and M. Padilla, “A prior-free framework of coherent inference and its derivation of simple shrinkage estimators,” Journal of Statistical Planning and Inference 145, 204–221 (2014). 2012 version

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Estimates of the local FDR

13 February 2013 Leave a comment

Z. Yang, Z. Li, and D. R. Bickel, “Empirical Bayes estimation of posterior probabilities of enrichment: A comparative study of five estimators of the local false discovery rate,” BMC Bioinformatics 14, art. 87 (2013). published version |  2011 version | 2010 version

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This paper adapts novel empirical Bayes methods for the problem of detecting enrichment in the form of differential representation of genes associated with a biological category with respect to a list of genes identified as differentially expressed. Read more…

MLE of the local FDR

13 February 2013 Comments off

Y. Yang, F. A. Aghababazadeh, and D. R. Bickel, “Parametric estimation of the local false discovery rate for identifying genetic associations,” IEEE/ACM Transactions on Computational Biology and Bioinformatics 10, 98-108 (2013). 2010 version | Slides

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Local FDR estimation for low-dimensional data

18 October 2012 Leave a comment

M. Padilla and D. R. Bickel, “Estimators of the local false discovery rate designed for small numbers of tests,” Statistical Applications in Genetics and Molecular Biology 11 (5), art. 4 (2012). Full article | 2010 & 2012 preprints

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This article describes estimators of local false discovery rates, compares their biases for small-scale inference, and illustrates the methods using a quantitative proteomics data set. In addition, theoretical results are presented in the appendices.

Local FDR estimation software

30 June 2012 1 comment

LFDRenrich is a suite of R functions for the estimation of local false discovery rates by maximum likelihood under a two-component or three-component parametric mixture model of 2X2 tables such as those used in gene enrichment analyses.

LFDRhat is a more general suite of R functions for the estimation of local false discovery rates by maximum likelihood under a two-component or three-component parametric mixture model.