Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  la Rosa, Patricio S ^a   Brooks, J Paul ^b   Deych, Elena ^a   Boone, Edward L ^b   Edwards, David J ^b   Wang, Qin ^b   Sodergren, Erica ^a   Weinstock, George ^a   Shannon, William D ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; BIOSTATISTICS; CALCULATION; COMPUTER PROGRAM; CONTROLLED STUDY; DATA BASE; EXPERIMENTAL DESIGN; FEMALE; GENE SEQUENCE; GEOGRAPHY; GINGIVA; HUMAN; HYPOTHESIS; MALE; MANTEL HAENSZEL TEST; METAGENOMICS; MICROBIOME; PHYLOGENY; SALIVA; SAMPLE SIZE; STATISTICAL ANALYSIS; STATISTICAL MODEL; TAXONOMY;

ADOLESCENT; ADULT; ALGORITHMS; BACTERIA; BIODIVERSITY; COMPUTATIONAL BIOLOGY; FEMALE; GINGIVA; HUMANS; MALE; METAGENOME; MODELS, STATISTICAL; REPRODUCIBILITY OF RESULTS; YOUNG ADULT;

EID: 84871441270     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0052078     Document Type: Article

References (34)

1. Peterson J, Garges S, Giovanni M, McInnes P, Wang L, et al. (2009) The NIH Human Microbiome Project. Genome Research 19: 2317-2323.
2. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, et al. (2007) The human microbiome project. Nature 449: 804-810.
3. Wooley JC, Godzik A, Friedberg I, (2010) A Primer on Metagenomics. PLoS Comput Biol 6: e1000667.
4. Singleton DR, Furlong MA, Rathbun SL, Whitman WB, (2001) Quantitative Comparisons of 16S rRNA Gene Sequence Libraries from Environmental Samples. Appl Environ Microbiol 67: 4374-4376.
5. Martin AP, (2002) Phylogenetic Approaches for Describing and Comparing the Diversity of Microbial Communities. Appl Environ Microbiol 68: 3673-3682.
6. Schloss PD, Larget BR, Handelsman J, (2004) Integration of Microbial Ecology and Statistics: a Test To Compare Gene Libraries. Appl Environ Microbiol 70: 5485-5492.
7. Lozupone C, Knight R, (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
8. Schloss PD, Handelsman J, (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-1506.
9. Schloss PD, Handelsman J, (2006) Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures. Appl Environ Microbiol 72: 6773-6779.
10. Schloss PD, Handelsman J, (2006) Introducing TreeClimber, a test to compare microbial community structures. Appl Environ Microbiol 72: 2379-2384.
11. Hamady M, Lozupone C, Knight R, (2009) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4: 17-27.
12. White JR, Nagarajan N, Pop M, (2009) Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples. PLoS Comput Biol 5: e1000352.
13. Mantel N, (1967) The detection of disease clustering and a generalized regression approach. Cancer research 27: 209-220.
14. Mantel N, Valand RS (1970) A technique of nonparametric multivariate analysis. Biometrics: 547-558.
15. Clarke KR, (1993) Non-parametric multivariate analyses of changes in community structure. Australian journal of ecology 18: 117-143.
16. Anderson MJ, (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecology 26: 32-46.
17. Holmes I, Harris K, Quince C, (2012) Dirichlet multinomial mixtures: generative models for microbial metagenomics. PLoS One 7: e30126.
18. La Rosa PS, Deych E, Shands B, Shannon WD (2011) HMP: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP. R-package.
19. Human Microbiome Project 16S rRNA Clinical Production Pilot (ID: 48335). pp. The NCBI BioProject website. Available: http://www.ncbi.nlm.nih.gov/bioproject?term=48335. Accessed 18 Sep 2012.
20. Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, et al. (2005) The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Research 33: D294-D296.
21. Vilo C, Dong Q (2012) Evaluation of the RDP Classifier Accuracy Using 16S rRNA Gene Variable Regions. Metagenomics.
22. Cox DR, (1983) Some remarks on overdispersion. Biometrika 70: 269-274.
23. Brier SS, (1980) Analysis of contingency table under cluster sampling. Biometrika 67: 591-596.
24. Tvedebrink T, (2010) Overdispersion in allelic counts and theta-correction in forensic genetics. Theor Popul Biol 78: 200-210.
25. Mosimann JE, (1962) On the compound multinomial distribution, the multivariate β-distribution, and correlations among proportions. Biometrika 49: 65-82.
26. Whittaker R, (1965) Dominance and diversity in land plant communities. Science 147: 250.
27. Magurran AE (2004) Measuring biological diversity: Wiley-Blackwell.
28. McGill BJ, Etienne RS, Gray JS, Alonso D, Anderson MJ, et al. (2007) Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework. Ecol Lett 10: 995-1015.
29. Legendre P (1998) Numerical ecology. Developments in environmental modelling.
30. Weir BS, Hill WG, (2002) ESTIMATING F-STATISTICS. Annual Review of Genetics 36: 721-750.
31. Kim BS, Margolin BH, (1992) Testing Goodness of Fit of a Multinomial Model Against Overdispersed Alternatives. Biometrics 48: 711-719.
32. Koehler K.J., Wilson JR, (1986) Chi-square tests for comparing vectors of proportions for several cluster samples. Communications in statistics Theory and Methods 15: 2977-2990.
33. Wilson JR, Koehler KJ (1984) Testing of equality of vectors of proportions for several cluster samples. Proceedings of Joint Statistical Association Meetings Survey Research Methods.
34. Kirk RE (1968) Experimental Design. Belmont: Wadsworth Inc.