Showing papers by "Valen E. Johnson published in 2017"
Posted Content•
TL;DR: This article proposed to change the default P-value threshold for statistical significance for claims of new discoveries from 0.05 to 0.005, which is the threshold used in this paper.
Abstract: We propose to change the default P-value threshold for statistical significance for claims of new discoveries from 0.05 to 0.005.
1,415 citations
TL;DR: The results of this reanalysis provide a compelling argument for both increasing the threshold required for declaring scientific discoveries and for adopting statistical summaries of evidence that account for the high proportion of tested hypotheses that are false.
Abstract: Investigators from a large consortium of scientists recently performed a multi-year study in which they replicated 100 psychology experiments. Although statistically significant results were reported in 97% of the original studies, statistical significance was achieved in only 36% of the replicated studies. This article presents a reanalysis of these data based on a formal statistical model that accounts for publication bias by treating outcomes from unpublished studies as missing data, while simultaneously estimating the distribution of effect sizes for those studies that tested nonnull effects. The resulting model suggests that more than 90% of tests performed in eligible psychology experiments tested negligible effects, and that publication biases based on p-values caused the observed rates of nonreproducibility. The results of this reanalysis provide a compelling argument for both increasing the threshold required for declaring scientific discoveries and for adopting statistical summaries of e...
131 citations
Posted Content•
TL;DR: The authors proposed to change the default P-value threshold for statistical significance for claims of new discoveries from 0.05 to 0.005, which is the threshold used in this paper.
Abstract: We propose to change the default P-value threshold for statistical significance for claims of new discoveries from 0.05 to 0.005.
14 citations
TL;DR: In this paper, a Bayesian variable selection procedure that uses a mixture prior composed of a point mass at zero and an inverse moment prior in conjunction with the partial likelihood defined by the Cox proportional hazard model is presented.
Abstract: Efficient variable selection in high-dimensional cancer genomic studies is critical for discovering genes associated with specific cancer types and for predicting response to treatment. Censored survival data is prevalent in such studies. In this article we introduce a Bayesian variable selection procedure that uses a mixture prior composed of a point mass at zero and an inverse moment prior in conjunction with the partial likelihood defined by the Cox proportional hazard model. The procedure is implemented in the R package BVSNLP, which supports parallel computing and uses a stochastic search method to explore the model space. Bayesian model averaging is used for prediction. The proposed algorithm provides better performance than other variable selection procedures in simulation studies, and appears to provide more consistent variable selection when applied to actual genomic datasets.
Posted Content•
08 Dec 2017
TL;DR: In this paper, a Bayesian variable selection procedure that uses a mixture prior composed of a point mass at zero and an inverse moment prior in conjunction with the partial likelihood defined by the Cox proportional hazard model is presented.
Abstract: Efficient variable selection in high-dimensional cancer genomic studies is critical for discovering genes associated with specific cancer types and for predicting response to treatment. Censored survival data is prevalent in such studies. In this article we introduce a Bayesian variable selection procedure that uses a mixture prior composed of a point mass at zero and an inverse moment prior in conjunction with the partial likelihood defined by the Cox proportional hazard model. The procedure is implemented in the R package BVSNLP, which supports parallel computing and uses a stochastic search method to explore the model space. Bayesian model averaging is used for prediction. The proposed algorithm provides better performance than other variable selection procedures in simulation studies, and appears to provide more consistent variable selection when applied to actual genomic datasets.