Two-group comparisons of zero-inflated intensity values: The choice of test statistic matters

Bioinformatics

Volumn 31, Issue 14, 2015, Pages 2310-2317

  Gleiss, Andreas ^a   Dakna, Mohammed ^b   Mischak, Harald ^b   Heinze, Georg ^a  

^a MEDICAL UNIVERSITY OF VIENNA   (Austria)

^b MOSAIQUES DIAGNOSTICS GMBH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE;

METABOLISM; NONPARAMETRIC TEST; STATISTICAL MODEL;

LIKELIHOOD FUNCTIONS; MODELS, STATISTICAL; PEPTIDES; STATISTICS, NONPARAMETRIC;

EID: 84941650273     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv154     Document Type: Article

References (16)

1. 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, 57, 289-300.
2. Coon, J. J. et al. (2008) CE-MS analysis of the human urinary proteome for biomarker discovery and disease diagnostics. Proteom. Clin. Appl., 2, 964-973.
3. Dakna, M. et al. (2010): Addressing the challenge of defining valid proteomic biomarkers and classifiers. BMC Bioinformatics, 11, 594-609.
4. Hallstrom, A. P. (2010) A modified Wilcoxon test for non-negative distributions with a clump of zeros. Stat. Med., 29, 391-400.
5. Helsel, D. R. (2012) Statistics for Censored Environmental Data Using MinitabVR and R. 2nd edn. Wiley, Hoboken.
6. Kerr, K. F. (2009) Comments on the analysis of unbalanced microarray data. Bioinformatics, 25, 2035-2041.
7. Lachenbruch, P. A. (1976) Analysis of data with clumping at zero. Biometr. Z., 18, 351-356.
8. Lachenbruch, P. A. (2001) Comparison of two-part models with competitors. Stat. Med., 20, 1215-1234.
9. Moulton, L. U. and Halsey, N. A. (1995) A mixture model with detection limits for regression analyses of antibody response to vaccine. Biometrics, 51, 1570-1578.
10. Neuhäuser, M. et al. (2005) Two-part permutation tests for DNA methylation and microarray data. BMC Bioinformatics, 6, 35-41.
11. Siwy, J. et al. (2011) Human urinary peptide database for multiple disease biomarker discovery. Proteom. Clin. Appl., 5, 367-374.
12. Smyth, G. K. (2005) Limma: linear models for microarray data. In: Gentleman, R. et al. (eds.) Bioinformatics and Computational Biology Solutions using R and Bioconductor. Springer, New York, pp. 397-420.
13. Taylor, S. and Pollard, K. (2009) Hypothesis tests for point-mass mixture data with application tó omics data with many zero values. Stat. Appl. Genet. Mo. B., 8, 1-43.
14. Tusher, V. et al. (2001) Significance analysis of microarrays applied to transcriptional responses to ionizing radiation. Proc. Natl. Acad. Sci. USA, 98, 5116-121.
15. Yang, Y. and Simpson, D. G. (2010) Conditional decomposition diagnostics for regression analysis of zero-inflated and left-censored data. Stat. Methods Med. Res., 21, 393-408.
16. Zhang, D. et al. (2009) Nonparametric methods for measurements below detection limit. Stat. Med., 28, 700-715.