P-values are being computed for increasingly complicated statistics but lacking evaluations on their quality. Meanwhile, accurate p-values enable significance comparison across batches of hypothesis tests and consequently unified false discover rate (FDR) control. This article discusses two related questions in this setting. First, we propose statistical tests to evaluate the quality of p-value  and the cross-batch comparability of any other statistic. Second, we propose a lasso based variable selection statistic, based on when the predictor variable first becomes active, and compute its p-value to achieve unified FDR control across multiple selections. In the end, we apply our tests on covTest, selectiveInference, and our statistic, based on real and null datasets for network inference in normal and high-dimensional settings. Results demonstrate higher p-value quality from our statistic and reveal p-value errors from others hidden before. We implement our statistic as lassopv in R .
Bayesian networks can represent directed gene regulations and therefore are favored over co-expression networks. However, hardly any Bayesian network study concerns the false discovery control (FDC) of network edges, leading to low accuracies due to systematic biases from inconsistent false discovery levels in the same study. We design four empirical tests to examine the FDC of Bayesian networks from three p-value based lasso regression variable selections --- two existing and one we originate. Our method, lassopv, computes p-values for the critical regularization strength at which a predictor starts to contribute to lasso regression. Using null and Geuvadis datasets, we find that lassopv obtains optimal FDC in Bayesian gene networks, whilst existing methods have defective p-values. The FDC concept and tests extend to most network inference scenarios and will guide the design and improvement of new and existing methods. Our novel variable selection method with lasso regression also allows FDC on other datasets and questions, even beyond network inference and computational biology. Lassopv is implemented in R and freely available at URL and URL
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P-values are being computed for increasingly complicated statistics but lacking evaluations on their quality. Meanwhile, accurate p-values enable significance comparison across batches of hypothesis tests and consequently unified false discover rate (FDR) control. This article discusses two related questions in this setting. First, we propose statistical tests to evaluate the quality of
Bayesian networks can represent directed gene regulations and therefore are favored over co-expression networks. However, hardly any Bayesian network study concerns the false discovery control (FDC) of network edges, leading to low accuracies due to systematic biases from inconsistent false discovery levels in the same study. We design four empirical tests to examine the FDC of Bayesian networks from three
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based lasso regression variable selections --- two existing and one we originate. Our method, lassopv, computes p-values for the critical regularization strength at which a predictor starts to contribute to lasso regression. Using null and Geuvadis datasets, we find that lassopv obtains optimal FDC in Bayesian gene networks, whilst existing methods have defective p-values. The FDC concept and tests extend to most network inference scenarios and will guide the design and improvement of new and existing methods. Our novel variable selection method with lasso regression also allows FDC on other datasets and questions, even beyond network inference
R
the cross-batch comparability of any other statistic. Second, we propose a lasso based variable selection statistic, based on when the predictor variable first becomes active, and compute its p-value to achieve unified FDR control across multiple selections. In the end, we apply our tests on covTest, selectiveInference, and our statistic, based on real and null datasets for network inference in normal and high-dimensional settings. Results demonstrate higher p-value quality from our statistic and reveal p-value errors from others hidden before. We implement our statistic as lassopv in R .
computational biology. Lassopv is implemented in R and freely available at URL and URL