Bioinformatics Vol. 19 no. 10 2003
Pages 1236-1242
© 2003 Oxford University Press
Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values
1 Department of Biostatistics
2 Departments of Pathology and Hematology/Oncology,
St. Jude Children’s Research Hospital, 332 N. Lauderdale St., Memphis, TN 38105-2794, USA
Received on October 18, 2002
; revised on January 10, 2003
; accepted on January 22, 2003
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: 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.
Availability: An S-plus function library is available from http://www.stjuderesearch.org/statistics
Contact: stanley.pounds{at}stjude.org
* To whom correspondence should be addressed.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  L. Zhang, J. J. Lee, H. Tang, Y.-H. Fan, L. Xiao, H. Ren, J. Kurie, R. C. Morice, W. K. Hong, and L. Mao Impact of Smoking Cessation on Global Gene Expression in the Bronchial Epithelium of Chronic Smokers Cancer Prevention Research, July 1, 2008; 1(2): 112 - 118. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. T. Dittrich, G. W. Klau, A. Rosenwald, T. Dandekar, and T. Muller Identifying functional modules in protein-protein interaction networks: an integrated exact approach Bioinformatics, July 1, 2008; 24(13): i223 - i231. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Karisik, M. J. Ellington, D. M. Livermore, and N. Woodford Virulence factors in Escherichia coli with CTX-M-15 and other extended-spectrum -lactamases in the UK J. Antimicrob. Chemother., January 1, 2008; 61(1): 54 - 58. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Pusztai, K. Anderson, and K. R. Hess Pharmacogenomic Predictor Discovery in Phase II Clinical Trials for Breast Cancer Clin. Cancer Res., October 15, 2007; 13(20): 6080 - 6086. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Lai A moment-based method for estimating the proportion of true null hypotheses and its application to microarray gene expression data Biostat., October 1, 2007; 8(4): 744 - 755. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C.-F. Chen and C.-H. Cheng Regulation of Cellular Metabolism and Cytokines by the Medicinal Herb Feverfew in the Human Monocytic THP-1 Cells Evid. Based Complement. Altern. Med., June 11, 2007; (2007) nem061v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Nakamura, I. J. Fidler, and K. R. Coombes Gene Expression Profile of Metastatic Human Pancreatic Cancer Cells Depends on the Organ Microenvironment Cancer Res., January 1, 2007; 67(1): 139 - 148. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. R. Hess, K. Anderson, W. F. Symmans, V. Valero, N. Ibrahim, J. A. Mejia, D. Booser, R. L. Theriault, A. U. Buzdar, P. J. Dempsey, et al. Pharmacogenomic Predictor of Sensitivity to Preoperative Chemotherapy With Paclitaxel and Fluorouracil, Doxorubicin, and Cyclophosphamide in Breast Cancer J. Clin. Oncol., September 10, 2006; 24(26): 4236 - 4244. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Pusztai, C. Mazouni, K. Anderson, Y. Wu, and W. F. Symmans Molecular Classification of Breast Cancer: Limitations and Potential Oncologist, September 1, 2006; 11(8): 868 - 877. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Pounds and C. Cheng Robust estimation of the false discovery rate Bioinformatics, August 15, 2006; 22(16): 1979 - 1987. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Gao Construction of null statistics in permutation-based multiple testing for multi-factorial microarray experiments Bioinformatics, June 15, 2006; 22(12): 1486 - 1494. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. B. Pounds Estimation and control of multiple testing error rates for microarray studies Brief Bioinform, March 1, 2006; 7(1): 25 - 36.
|
|
|
|
|
|
R. Luthra, T.-T. Wu, M. G. Luthra, J. Izzo, E. Lopez-Alvarez, L. Zhang, J. Bailey, J. H. Lee, R. Bresalier, A. Rashid, et al. Gene Expression Profiling of Localized Esophageal Carcinomas: Association With Pathologic Response to Preoperative Chemoradiation J. Clin. Oncol., January 10, 2006; 24(2): 259 - 267. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-D. Zhang and T. W. Gant Effect of pooling samples on the efficiency of comparative studies using microarrays Bioinformatics, December 15, 2005; 21(24): 4378 - 4383. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Xie, W. Pan, and A. B. Khodursky A note on using permutation-based false discovery rate estimates to compare different analysis methods for microarray data Bioinformatics, December 1, 2005; 21(23): 4280 - 4288. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Pounds and C. Cheng Sample size determination for the false discovery rate Bioinformatics, December 1, 2005; 21(23): 4263 - 4271. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Hu, M. Kapoor, W. Zhang, S. R. Hamilton, and K. R. Coombes Analysis of dose-response effects on gene expression data with comparison of two microarray platforms Bioinformatics, September 1, 2005; 21(17): 3524 - 3529. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. V. Abruzzo, J. Wang, M. Kapoor, L. J. Medeiros, M. J. Keating, W. E. Highsmith, L. L. Barron, C. C. Cromwell, and K. R. Coombes Biological Validation of Differentially Expressed Genes in Chronic Lymphocytic Leukemia Identified by Applying Multiple Statistical Methods to Oligonucleotide Microarrays J. Mol. Diagn., August 1, 2005; 7(3): 337 - 345. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Stec, J. Wang, K. Coombes, M. Ayers, S. Hoersch, D. L. Gold, J. S Ross, K. R. Hess, S. Tirrell, G. Linette, et al. Comparison of the Predictive Accuracy of DNA Array-Based Multigene Classifiers across cDNA Arrays and Affymetrix GeneChips J. Mol. Diagn., August 1, 2005; 7(3): 357 - 367. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Datta and S. Datta Empirical Bayes screening of many p-values with applications to microarray studies Bioinformatics, May 1, 2005; 21(9): 1987 - 1994. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Diez-Tascon, O. M. Keane, T. Wilson, A. Zadissa, D. L. Hyndman, D. B. Baird, J. C. McEwan, and A. M. Crawford Microarray analysis of selection lines from outbred populations to identify genes involved with nematode parasite resistance in sheep Physiol Genomics, March 21, 2005; 21(1): 59 - 69. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Dalmasso, P. Broët, and T. Moreau A simple procedure for estimating the false discovery rate Bioinformatics, March 1, 2005; 21(5): 660 - 668. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Koomen, L. N. Shih, K. R. Coombes, D. Li, L.-c. Xiao, I. J. Fidler, J. L. Abbruzzese, and R. Kobayashi Plasma Protein Profiling for Diagnosis of Pancreatic Cancer Reveals the Presence of Host Response Proteins Clin. Cancer Res., February 1, 2005; 11(3): 1110 - 1118. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Pusztai and K. R. Hess Clinical trial design for microarray predictive marker discovery and assessment Ann. Onc., December 1, 2004; 15(12): 1731 - 1737. [Abstract] [Full Text] [PDF]
|
|