Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values
Stan Pounds,Stephan W. Morris +1 more
TLDR
The occurrence of false positives and false negatives in a microarray analysis could be easily estimated if the distribution of p-values were approximated and then expressed as a mixture of null and alternative densities.Abstract:
Motivation: The occurrence of false positives and false negatives in a microarray analysis could be easily estimated if the distribution of p-values were approximated and then expressed as a mixture of null and alternative densities. Essentially any distribution of p-values can be expressed as such a mixture by extracting a uniform density from it. Results: Am odel is introduced that frequently describes very accurately the distribution of a set of p-values arising from an array analysis. The model is used to obtain an estimated distribution that is easily expressed as a mixture of null and alternative densities. Given a threshold of significance, the estimated distribution is partitioned into regions corresponding to the occurrences of false positives, false negatives, true positives, and true negatives. Availability: An S-plus function library is available fromread more
Citations
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Microarray data analysis: from disarray to consolidation and consensus.
TL;DR: In just a few years, microarrays have gone from obscurity to being almost ubiquitous in biological research, and points of consensus are emerging about the general approaches that warrant use and elaboration.
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Distinct Cellular Mechanisms Underlie Anti-CTLA-4 and Anti-PD-1 Checkpoint Blockade
Spencer C. Wei,Jacob H. Levine,Alexandria P. Cogdill,Yang Zhao,Nana Ama A.S. Anang,Miles C. Andrews,Padmanee Sharma,Jing Wang,Jennifer A. Wargo,Dana Pe'er,James P. Allison +10 more
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Analysis of Immune Signatures in Longitudinal Tumor Samples Yields Insight into Biomarkers of Response and Mechanisms of Resistance to Immune Checkpoint Blockade.
Pei Ling Chen,Whijae Roh,Alexandre Reuben,Zachary A. Cooper,Christine N. Spencer,Peter A. Prieto,John P. Miller,Roland L. Bassett,Vancheswaran Gopalakrishnan,Khalida Wani,Mariana Petaccia de Macedo,Jacob Austin-Breneman,Hong Jiang,Qing Chang,Sangeetha M. Reddy,Wei Shen Chen,Michael T. Tetzlaff,Russell J. Broaddus,Michael A. Davies,Jeffrey E. Gershenwald,Lauren E. Haydu,Alexander J. Lazar,Sapna Pradyuman Patel,Patrick Hwu,Wen-Jen Hwu,Adi Diab,Isabella C. Glitza,Scott E. Woodman,Luis M Vence,Ignacio I. Wistuba,Rodabe N. Amaria,Lawrence N. Kwong,Victor G. Prieto,R. Eric Davis,Wencai Ma,Willem W. Overwijk,Arlene H. Sharpe,Jianhua Hu,P. Andrew Futreal,Jorge Blando,Padmanee Sharma,James P. Allison,Lynda Chin,Jennifer A. Wargo +43 more
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Pharmacogenomic Predictor of Sensitivity to Preoperative Chemotherapy With Paclitaxel and Fluorouracil, Doxorubicin, and Cyclophosphamide in Breast Cancer
Kenneth R. Hess,Keith Anderson,W. Fraser Symmans,Vicente Valero,Nuhad K. Ibrahim,Jaime A. Mejia,Daniel J. Booser,Richard L. Theriault,Aman U. Buzdar,Peter J. Dempsey,Roman Rouzier,Nour Sneige,Jeffrey S. Ross,Tatiana Vidaurre,Henry L. Gomez,Gabriel N. Hortobagyi,Lajos Pusztai +16 more
TL;DR: A 30-probe set pharmacogenomic predictor predicted pCR to T/FAC chemotherapy with high sensitivity and negative predictive value.
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Identifying functional modules in protein–protein interaction networks
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