MultiTest V.1.2, a program to binomially combine independent tests and performance comparison with other related methods on proportional data

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  De Meeûs, Thierry ^a,b   Guégan, Jean François ^b   Teriokhin, Anatoly T ^c  

^a Institut de recherche pour le développement   (Burkina Faso)

^b UNIV MONTPELLIER   (France)

^c MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

BONFERRONI PROCEDURE; CLONAL REPRODUCTION; LINKAGE DISEQUILIBRIUM; PERFORMANCE COMPARISON; POPULATION GENETICS; PROPORTIONAL DATUM; PUBLICATION BIAS; SIGNAL STRENGTHS;

CHROMOSOMES; POPULATION STATISTICS; STATISTICAL TESTS;

SOFTWARE TESTING;

ARTICLE; COMPARATIVE STUDY; COMPUTER PROGRAM; GENE EXPRESSION PROFILING; METHODOLOGY; POPULATION GENETICS; STATISTICAL MODEL;

GENE EXPRESSION PROFILING; GENETICS, POPULATION; MODELS, STATISTICAL; SOFTWARE;

EID: 75649110365     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-443     Document Type: Article

References (36)

1. Holm S. A simple sequentially rejective multiple test procedure. Scandinavian Journal of Statistics 1979, 6:65-70.
2. Rice WR. Analyzing tables of statistical tests. Evolution 1989, 43:223-225.
3. Benjamini Y, Hochberg Y. On the adaptive control of the false discovery fate in multiple testing with independent statistics. Journal of Educational and Behavioral Statistics 2000, 25:60-83.
4. Abila PP, Slotman MA, Parmakelis A, Dion KB, Robinson AS, Muwanika VB, Enyaru JCK, Lokedi LM, Aksoy S, Caccone A. High levels of genetic differentiation between Ugandan Glossina fuscipes fuscipes populations separated by Lake Kyoga. PLoS Negl Trop Dis 2008, 2:e242. 10.1371/journal.pntd.0000242, 2386243, 18509474.
5. Ouma JO, Marquez JG, Krafsur ES. Microgeographical breeding structure of the tsetse fly, Glossina pallidipes in south-western Kenya. Med Vet Entomol 2006, 20:138-149. 10.1111/j.1365-2915.2006.00609.x, 1450340, 16608498.
6. Ouma JO, Marquez JG, Krafsur ES. Patterns of genetic diversity and differentiation in the tsetse fly Glossina morsitans morsitans Westwood populations in East and southern Africa. Genetica 2007, 130:139-151. 10.1007/s10709-006-9001-0, 2519096, 16897444.
7. Hansen MM, Nielsen EE, Mensberg KLD. The problem of sampling families rather than populations: relatedness among individuals in samples of juvenile brown trout Salmo trutta L. Mol Ecol 1997, 6:469-474.
8. Estoup A, Tailliez C, Cornuet JM, Solignac M. Size homoplasy and mutational processes of interrupted microsatellites in two bee species, Apis mellifera and Bombus terrestris (Apidae). Mol Biol Evol 1995, 12:1074-1084.
9. Fisher RA. Statistical Methods for Research Workers 1970, Edinburgh: Oliver and Boyd, 14.
10. Manly BFJ. The Statistics of Natural Selection 1985, London: Chapman & Hall.
11. Bender R, Lange S. Adjusting for multiple testing - when and how?. J Clin Epidemiol 2001, 54:343-349. 10.1016/S0895-4356(00)00314-0, 11297884.
12. Nakagawa S. A farewell to Bonferroni: the problems of low statistical power and publication bias. Behav Ecol 2004, 15:1044-1045.
13. Teriokhin AT, De Meeûs T, Guegan JF. On the power of some binomial modifications of the Bonferroni multiple test. Zh Obshch Biol 2007, 68:332-340.
14. Verhoeven KJF, Simonsen KL, McIntyre LM. Implementing false discovery rate control: increasing your power. Oikos 2005, 108:643-647.
15. Goudet J. An improved procedure for testing the effects of key innovations on rate of speciation. Am Nat 1999, 153:549-555.
16. Whitlock MC. Combining probability from independent tests: the weighted Z-method is superior to Fisher's approach. J Evol Biol 2005, 18:1368-1373. 10.1111/j.1420-9101.2005.00917.x, 16135132.
17. Rice WR. A consensus combined P-Value test and the family-wide significance of component tests. Biometrics 1990, 46:303-308.
18. Wilkinson B. A statistical consideration in psychological research. Psychol Bull 1951, 48:156-158. 10.1037/h0059111, 14834286.
19. Prugnolle F, De Meeûs T, Durand P, Sire C, Théron A. Sex-specific genetic structure in Schistosoma mansoni: evolutionary and epidemiological implications. Mol Ecol 2002, 11:1231-1238. 10.1046/j.1365-294X.2002.01518.x, 12074730.
20. Balloux F. EASYPOP (version 1.7): A computer program for population genetics simulations. J Hered 2001, 92:301-302. 10.1093/jhered/92.3.301, 11447253.
21. Goudet J, Raymond M, De Meeûs T, Rousset F. Testing differentiation in diploid populations. Genetics 1996, 144:1933-1940. 1207740, 8978076.
22. Goudet J. FSTAT (Version 1.2): A computer program to calculate F-statistics. J Hered 1995, 86:485-486.
23. De Meeûs T, McCoy KD, Prugnolle F, Chevillon C, Durand P, Hurtrez-Boussès S, Renaud F. Population genetics and molecular epidemiology or how to "débusquer la bête". Infect Genet Evol 2007, 7:308-332. 10.1016/j.meegid.2006.07.003, 16949350.
24. Raymond M, Rousset F. Genepop (Version-1.2) - Population-Genetics Software for Exact Tests and Ecumenicism. J Hered 1995, 86:248-249.
25. Rousset F. GENEPOP '007: a complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources 2008, 8:103-106.
26. Rousset F, Raymond M. Statistical analyses of population genetic data: New tools, old concepts. Trends Ecol Evol 1997, 12:313-317.
27. De Meeûs T, Balloux F. Clonal reproduction and linkage disequilibrium in diploids: a simulation study. Infect Genet Evol 2004, 4:345-351. 10.1016/j.meegid.2004.05.002, 15374532.
28. Škalamera JP, Renaud F, Raymond M, De Meeûs T. No evidence for genetic differentiation of the mussel Mytilus galloprovincialis between lagoons and the seaside. Marine Ecology-Progress Series 1999, 178:251-258.
29. Raymond M, Vaanto RL, Thomas F, Rousset F, deMeeus T, Renaud F. Heterozygote deficiency in the mussel Mytilus edulis species complex revisited. Mar Ecol Prog Ser 1997, 156:225-237.
30. Nébavi F, Ayala FJ, Renaud F, Bertout S, Eholié S, Moussa K, Mallié M, De Meeûs T. Clonal population structure and genetic diversity of Candida albicans in AIDS patients from Abidjan (Cote d'Ivoire). Proc Natl Acad Sci USA 2006, 103:3663-3668. 10.1073/pnas.0511328103, 1450139, 16501044.
31. Slowinski JB, Guyer C. Testing whether certain traits have caused amplified diversification: an improved method based on a model of random speciation and extinction. Am Nat 1993, 142:1019-1024. 10.1086/285586, 19425946.
32. Savolainen V, Goudet J. Rate of gene sequence evolution and species diversification in flowering plants: a re-evaluation. Proceedings of the Royal Society of London Series B-Biological Sciences 1998, 265:603-607.
33. Thomas F, Renaud F, De Meeûs T, Poulin R. Manipulation of host behaviour by parasites: ecosystem engineering in the intertidal zone?. Proceedings of the Royal Society of London Series B-Biological Sciences 1998, 265:1091-1096.
34. Dib L, Bitam I, Tahri M, Bensouilah M, De Meeûs T. Competitive exclusion between piroplasmosis and anaplasmosis agents within cattle. PLoS Pathog 2008, 4:2-5.
35. De Garine-Wichatitsky M, De Meeûs T, Chevillon C, Berthier D, Barre N, Thévenon S, Maillard JC. Population genetic structure of wild and farmed rusa deer (Cervus timorensis russa) in New-Caledonia inferred from polymorphic microsatellite loci. Genetica 2009, 137:313-323. 10.1007/s10709-009-9395-6, 19680748.
36. Chevillon C, Koffi BB, Barré N, Durand P, Arnathau C, De Meeûs T. Direct and indirect inferences on parasite mating and gene transmission patterns. Pangamy in the cattle tick Rhipicephalus (Boophilus) microplus. Infect Genet Evol 2007, 7:298-304. 10.1016/j.meegid.2006.11.007, 17215171.