Discrete nonparametric algorithms for outlier detection with genomic data

Journal of Biopharmaceutical Statistics

Volumn 20, Issue 2, 2010, Pages 193-208

  Ghosh, Debashis ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Cancer genomics; False discovery rate; Gene fusion; Marginal distributions; Multiple testing; Stability

Indexed keywords

ALGORITHM; ARTICLE; CANCER GENETICS; GENE EXPRESSION; GENE EXPRESSION PROFILING; METHODOLOGY; NONPARAMETRIC TEST; PRIORITY JOURNAL; PROSTATE CANCER; SEQUENTIAL ANALYSIS; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE; THEORETICAL MODEL;

ALGORITHMS; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOMICS; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; MALE; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROSTATIC NEOPLASMS; REPRODUCIBILITY OF RESULTS; STATISTICS, NONPARAMETRIC;

EID: 77951286626     PISSN: 10543406     EISSN: 15205711     Source Type: Journal    
DOI: 10.1080/10543400903572704     Document Type: Article

References (24)

1. Benjamini, Y., Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B 57:289-300.
2. Chi, Z. (2008). False discovery control with multivariate p values. Electronic Journal of Statistics 2:368-411.
3. Efron, B., Tibshirani, R., Storey, J. D., Tusher, V. (2001). Empirical Bayes analysis of a microarray experiment. Journal of the American Statistical Association 96:1151-1160.
4. Ferreira, J. A. (2007). The Benjamini-Hochberg method in the case of discrete test statistics. International Journal of Biostatistics 3(1):article 11.
5. Futreal, P. A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N., Stratton, M. R. (2004). A census of human cancer genes. Nature Reviews Genetics 4:177-183.
6. Garcia-Higuera, I., Taniguchi, T., Ganesan, S., Meyn, M. S., Timmers, C., Hejna, J., Grompe, M., D'Andrea, A. D. (2001). Interaction of the Fanconi anemia proteins and BRCA1 in a common pathway. Molecular Cell 7:249-262.
7. Ge, Y., Dudoit, S., Speed, T. P. (2003). Resampling-based multiple testing for microarray data analysis. Test 12:1-44.
8. Genovese, C. R., Wasserman, L. (2004). A stochastic process approach to false discovery control. Annals of Statistics 35:1035-1061.
9. Ghosh, D., Chinnaiyan, A. M. (2009). Genomic outlier profile analysis: mixture models, null hypotheses and nonparametric estimation. Biostatistics 10:60-69.
10. Gilbert, P. B. (2005). A modified false discovery rate multiple-comparisons procedure for discrete data, applied to human immunodeficiency virus genetics. Applied Statistics 54:143-158.
11. Hanahan, D., Weinberg, R. A. (2000). The hallmarks of cancer. Cell 100:57-70.
12. Hall, P., Wang, Q. (2009). Strong approximations of level exceedances related to multiple hypothesis testing. Unpublished technical report (in press).
13. Jones, K. A., Jiang, X., Yamamoto, Y., Yeung, R. S. (2004). Tuberin is a component of lipid rafts and mediates caveolin-1 localization: role of TSC2 in post-Golgi transport. Experiments in Cell Research 295:512-524.
14. Little, R. J. A., Rubin, D. B. (2002). Statistical Analysis with Missing Data. 2nd ed. New York: Wiley.
15. Liu, F., Wu, B. (2007). Multi-group cancer outlier differential gene expression detection. Computational Biology and Chemistry 31(2):65-71.
16. Ludwig, J. A., Weinstein, J. N. (2005). Biomarkers in cancer staging, prognosis and treatment. Nature Reviews Cancer 11:845-856.
17. Ploner, A., Calza, S., Gusnanto, A., Pawitan, Y. (2006). Multidimensional local false discovery rate for microarray studies. Bioinformatics 22(5):556-565.
18. Pounds, S., Cheng, C. (2006). Robust estimation of the false discovery rate. Bioinformatics 22:1979-1987.
19. Shaffer, J. (1995). Multiple hypothesis testing. Annual Reviews of Psychology 46:561-584.
20. Tarone, R. E. (1990). A modified Bonferroni method for discrete data. Biometrics 46:515-522.
21. Tibshirani, R., Hastie, T. (2007). Outlier sums for differential gene expression analysis. Biostatistics 8:2-8.
22. Tomlins, S. A., Rhodes, D. R., Perner, S., Dhanasekaran, S. M., Mehra, R., Sun, X. W., Varambally, S., Cao, X., Tchinda, J., Kuefer, R., Lee, C., Montie, J. E., Shah, R. B., Pienta, K. J., Rubin, M. A., Chinnaiyan, A. M. (2005). Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310:644-648.
23. Troyanskaya, O., Cantor, M., Sherlock, G., Brown, P., Hastie, T., Tibshirani, R., Botstein, D., Altman, R. B. (2001). Missing value estimation methods for DNA microarrays. Bioinformatics 17:520-525.
24. Wu, B. (2007). Cancer outlier differential gene expression detection. Biostatistics 8:566-575.