Sample size calculation for differential expression analysis of RNA-seq data under Poisson distribution

International Journal of Computational Biology and Drug Design

Volumn 6, Issue 4, 2013, Pages 358-375

  Li, Chung I ^a   Su, Pei Fang ^b   Guo, Yan ^c   Shyr, Yu ^c  

^a NATIONAL CHIAYI UNIVERSITY   (Taiwan)

^b NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

^c VANDERBILT UNIVERSITY   (United States)

Author keywords

False discovery rate; Poisson distribution; RNA seq; Sample size determination

Indexed keywords

ARTICLE; CALCULATION; GENE EXPRESSION; PERFORMANCE; POISSON DISTRIBUTION; QUANTITATIVE STUDY; RNA ANALYSIS; RNA SEQUENCE; SAMPLE SIZE; SIMULATION; MATHEMATICAL COMPUTING;

EID: 84885030144     PISSN: 17560756     EISSN: 17560764     Source Type: Journal    
DOI: 10.1504/IJCBDD.2013.056830     Document Type: Article

References (35)

1. Anders, S. and Huber, W. (2010) 'Differential expression analysis for sequence count data', Genome Biol., Vol. 11, No. 10, p. R106.
2. Auer, P.L. and Doerge, R.W. (2010) 'Statistical design and analysis of rna sequencing data', Genetics, Vol. 185, No. 2, pp. 405-416.
3. Benjamini, Y. and Hochberg, Y. (1995) 'Controlling the false discovery rate: a practical and powerful approach to multiple testing', J. R. Stat. Soc. Ser. B, Vol. 57, No. 1, pp. 289-300.
4. Blekhman, R., Marioni, J.C., Zumbo, P., Stephens, M. and Gilad, Y. (2010) 'Sex-specific and lineage-specific alternative splicing in primates', Genome Res., Vol. 20, No. 2, pp. 180-189.
5. Cloonan, N., Forrest, A. R. R., Kolle, G., Gardiner, B. B. A., Faulkner, G. J., Brown, M. K., Taylor, D. F., Steptoe, A. L., Wani, S., Bethel, G., Robertson, A. J., Perkins, A. C., Bruce, S. J., Lee, C. C., Ranade, S. S., Peckham, H. E., Manning, J. M., McKernan, K. J., and Grimmond, S. M. (2008) 'Stem cell transcriptome profiling via massive-scale mrna sequencing', Nat. Methods, Vol. 5, No. 7, pp. 613-619. (Pubitemid 351911866)
6. Fang, Z. and Cui, X. (2011) 'Design and validation issues in rna-seq experiments', Brief. Bioinform., Vol. 12, No. 3, pp. 280-287.
7. Griffith, M., Griffith, O. L., Mwenifumbo, J., Goya, R., Morrissy, A. S., Morin, R. D., Corbett, R., Tang, M. J., Hou, Y.-C., Pugh, T. J., Robertson, G., Chittaranjan, S., Ally, A., Asano, J. K., Chan, S. Y., Li, H. I., McDonald, H., Teague, K., Zhao, Y., Zeng, T., Delaney, A., Hirst, M., Morin, G. B., Jones, S. J. M., Tai, I. T., and Marra, M. A. (2010) 'Alternative expression analysis by rna sequencing', Nat. Methods, Vol. 7, No. 10, pp. 843-847.
8. Gu, K., Ng, H. K. T., Tang, M. L., and Schucany, W. R. (2008) 'Testing the ratio of two poisson rates', Biom. J., Vol. 50, No. 2, pp. 283-298.
9. Hashimoto, S.-i., Qu, W., Ahsan, B., Ogoshi, K., Sasaki, A., Nakatani, Y., Lee, Y., Ogawa, M., Ametani, A., Suzuki, Y., Sugano, S., Lee, C. C., Nutter, R. C., Morishita, S., and Matsushima, K. (2009) 'High-resolution analysis of the 5'-end transcriptome using a next generation dna sequencer', PLoS One, Vol. 4, No. 1, p.e4108.
10. Hirakawa, A., Sato, Y., Sozu, T., Hamada, C., and Yoshimura, I. (2007) 'Estimating the false discovery rate using mixed normal distribution for identifying differentially expressed genes in microarray data analysis', Cancer Inform., Vol. 3, pp. 140-148.
11. Hu, J., Zou, F., and Wright, F. A. (2005) 'Practical fdr-based sample size calculations in microarray experiment', Bioinformatics, Vol. 21, pp. 3264-3272. (Pubitemid 41418440)
12. Huffman, M. D. (1984) 'An improved approximate two-sample poisson test', J. R. Stat. Soc. Ser. B, Vol. 33, pp. 224-226.
13. Jiang, H. and Wong, W. H. (2009) 'Statistical inferences for isoform expression in rnaseq', Bioinformatics, Vol. 25, No. 8, pp. 1026-1032.
14. Jung, S.-H. (2005) 'Sample size for fdr-control in microarray data analysis', Bioinformatics, Vol. 21, No. 14, pp. 3097-3104. (Pubitemid 41418462)
15. Krishnamoorhy, K. and Thomson, J. (2004) 'A more powerful test for comparing two poisson means', J. Stat. Plan Infer., Vol. 119, pp. 23-35. (Pubitemid 37378881)
16. Li, B., Ruotti, V., Stewart, R. M., Thomson, J. A., and Dewey, C. N. (2010) 'Rnaseq gene expression estimation with read mapping uncertainty', Bioinformatics, Vol. 26, No. 4, pp. 493-500.
17. Li, J., Witten, D. M., Johnstone, I. M., and Tibshirani, R. (2011) 'Normalization, testing, and false discovery rate estimation for rna-sequencing data', Biostatistics, Vol. 14, pp. 1-16.
18. Liu, P. and Hwang, J. T. G. (2007) 'Quick calculation for sample size while controlling false discovery rate with application to microarray analysis', Bioinformatics, Vol. 23, No. 6, pp. 739-746. (Pubitemid 46554726)
19. Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M., and Gilad, Y. (2008) 'Rnaseq: an assessment of technical reproducibility and comparison with gene expression arrays', Genome Res., Vol. 18, No. 9, pp. 1509-1517.
20. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. (2008) 'Mapping and quantifying mammalian transcriptomes by rna-seq', Nat. Methods, Vol. 5, No. 7, pp. 621-628. (Pubitemid 351911867)
21. Ng, H. K. T. and Tang, M.-L. (2005) 'Testing the equality of two poisson means using the rate ratio', Stat. Med., Vol. 24, No. 6, pp. 955-965. (Pubitemid 40403177)
22. Pawitan, Y., Michiels, S., Koscielny, S., Gusnanto, A., and Ploner, A. (2005) 'False discovery rate, sensitivity and sample size for microarray studies', Bioinformatics, Vol. 21, pp. 3017-3024. (Pubitemid 40916427)
23. Pickrell, J. K., Marioni, J. C., Pai, A. A., Degner, J. F., Engelhardt, B. E., Nkadori, E., Veyrieras, J.-B., Stephens, M., Gilad, Y., and Pritchard, J. K. (2010) 'Understanding mechanisms underlying human gene expression variation with rna sequencing', Nature, Vol. 464, No. 7289, pp. 768-772.
24. Pounds, S. and Cheng, C. (2005) 'Sample size determination for the false discovery rate', Bioinformatics, Vol. 21, No. 23, pp. 4263-4271. (Pubitemid 41724306)
25. Robertson, G., Schein, J., Chiu, R., Corbett, R., Field, M., Jackman, S. D., Mungall, K., Lee, S., Okada, H. M., Qian, J. Q., Griffith, M., Raymond, A., Thiessen, N., Cezard, T., Butterfield, Y. S., Newsome, R., Chan, S. K., She, R., Varhol, R., Kamoh, B., Prabhu, A.-L., Tam, A., Zhao, Y., Moore, R. A., Hirst, M., Marra, M. A., Jones, S. J. M., Hoodless, P. A., and Birol, I. (2010) 'De novo assembly and analysis of rna-seq data', Nat. Methods, Vol. 7, No. 11, pp. 909-912.
26. Robinson, M. D. and Smyth, G. K. (2008) 'Small-sample estimation of negative binomial dispersion, with applications to sage data', Biostatistics, Vol. 9, No. 2, pp. 321-332. (Pubitemid 351438556)
27. Srivastava, S. and Chen, L. (2010) 'A two-parameter generalized poisson model to improve the analysis of rna-seq data', Nucleic Acids Res., Vol. 38, No. 17, p.e170.
28. Storey, J. D. (2002) 'A direct approach to false discovery rates', J. R. Stat. Soc. Ser. B, Vol. 64, No. 3, pp. 479-498.
29. Storey, J. D. and Tibshirani, R. (2001) Estimating false discovery rates under dependence, with applications to dna microarrays, Technical report, Department of Statistics, Standford University, CA.
30. Storey, J. D. and Tibshirani, R. (2003) 'Statistical significance for genomewide studies', Proc. Natl. Acad. Sci. U. S. A., Vol. 100, No. 16, pp. 9440-9445. (Pubitemid 37033947)
31. Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., and Pachter, L. (2010) 'Transcript assembly and quantification by rna-seq reveals unannotated transcripts and isoform switching during cell differentiation', Nat. Biotechnol., Vol. 28, No. 5, pp. 511-515.
32. Wang, L., Feng, Z., Wang, X., Wang, X., and Zhang, X. (2010a) 'Degseq: an r package for identifying differentially expressed genes from rna-seq data', Bioinformatics, Vol. 26, No. 1, pp. 136-138.
33. Wang, L., Xi, Y., Yu, J., Dong, L., Yen, L., and Li, W. (2010b) 'A statistical method for the detection of alternative splicing using rna-seq', PLoS One, Vol. 5, No. 1, p.e8529.
34. Wu, Z., Wang, X., and Zhang, X. (2011) 'Using non-uniform read distribution models to improve isoform expression inference in rna-seq', Bioinformatics, Vol. 27, No. 4, pp. 502-508.
35. Zhang, L., Zhou, W., Velculescu, V. E., Kern, S. E., Hruban, R. H., Hamilton, S. R., Vogelstein, B., and Kinzler, K. W. (1997) 'Gene expression profiles in normal and cancer cells', Science, Vol. 276, No. 5316, pp. 1268-1272. (Pubitemid 27227367)