Use of cluster separation indices and the influence of outliers: Application of two new separation indices, the modified silhouette index and the overlap coefficient to simulated data and mouse urine metabolomic profiles

Journal of Chemometrics

Volumn 23, Issue 1, 2009, Pages 19-31

  Dixon, Sarah J ^a   Heinrich, Nina ^b   Holmboe, Maria ^b   Schaefer, Michele L ^c   Reed, Randall R ^c   Trevejo, Jose ^b   Brereton, Richard G ^a  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

^b CHARLES STARK DRAPER LABORATORY   (United States)

^c JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Cluster separation; Davies bouldin index; Metabolomics; Outliers; Silhouette index; Simulations; Urine

Indexed keywords

BODY FLUIDS; GAS CHROMATOGRAPHY; MASS SPECTROMETRY; STATISTICS;

CLUSTER SEPARATION; DAVIES-BOULDIN INDEX; METABOLOMICS; OUTLIER; OVERLAP COEFFICIENTS; SEPARATION INDEX; SILHOUETTE INDICES; SILHOUETTE WIDTH; SIMULATION; URINE;

MAMMALS;

EID: 58549116509     PISSN: 08869383     EISSN: 1099128X     Source Type: Journal    
DOI: 10.1002/cem.1189     Document Type: Article

References (23)

1. Yamaguchi T, Shioji I, Sugimoto A, Yamaoka M. Psychological stress increases bilirubin metabolites in human urine. Biochem. Biophys. Res. Comm. 2002; 293: 517-520.
2. Sack RL, Lewy AJ, Erb DL, Vollmer WM, Singer CM. Human melatonin production decreases with age. J. Pineal Res. 1986; 3: 379-388.
3. Jemiolo B, Andreolini F, Wiesler D, Novotny M. Variations in mouse (Mus Musculus) urinary volatiles during different periods of pregnancy and lactation. J. Chem. Ecol. 1987; 13: 1941-1956.
4. Plumb R, Granger J, Stumpf G, Wilson ID, Evans JA, Lenz EM. Metabonomic analysis of mouse urine by liquid-chromatography-time of flight mass spectrometry (Lc-Tofms): detection of strain, diurnal and gender differences. Analyst 2003; 128: 819-823.
5. Kaufman L, Rousseeuw PJ. Finding Groups in Data: An Introduction to Cluster Analysis. Wiley: New York, 1990.
6. Davies DL, Bouldin DW. A cluster separation measure. IEEE Trans. Patt. Anal. Mach. Intell. 1979; 1: 224-227.
7. Rousseeuw PJ. Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J. Comput. Appl. Math. 1987; 20: 53-65.
8. Wu K-L, Yang M-S. A cluster validity index for fuzzy clustering. Patt. Recog. Lett. 2005; 26: 1275-1291.
9. Butler RW, Davies PL, Jhun M. Asymptotics for the minimum covariance determinant estimator. Ann. Stat. 1993; 21: 1385-1400.
10. Rousseeuw PJ, Leroy AM. Robust Regression and Outlier Detection. Wiley: New York, 1987.
11. Butler RW. Nonparametric interval and point prediction using data trimmed by a Grubbs type outlier rule. Ann. Stat. 1982; 10: 197-204.
12. Rousseeuw PJ, Driessen KV. A fast algorithm for the minimum covariance determinant estimator. Technometrics 1999; 41: 212-223.
13. Wongravee K, Heinrich N, Holmboe M, Schaefer ML, Reed RR, Trevejo J, Brereton RG. submitted.
14. Dixon SJ, Brereton RG, Soini HA, Novotny MV, Penn DJ. An automated method for peak detection and matching in large gas chromatography-mass spectrometry data sets. J. Chemom. 2007; 20: 325-340.
15. Dixon SJ, Xu Y, Brereton RG, Soini HA, Novotny MV, Oberzaucher E, Grammer K, Penn DJ. Pattern recognition of gas chromatography mass spectrometry of human volatiles in sweat to distinguish the sex of subjects and determine potential discriminatory marker peaks. Chemom. Intell. Lab. Syst. 2007; 87: 161-172.
16. Xu Y, Gong F, Dixon SJ, Brereton RG, Soini HA, Novotny MV, Oberzaucher E, Grammer K, Penn DJ. Application of dissimilarity indices, principal coordinates analysis, and rank tests to peak tables in metabolomics of the gas chromatography/mass spectrometry of human sweat. Anal. Chem. 2007; 79: 5633-5641.
17. Everitt BS. A Monte Carlo investigation of the robustness of Hotelling's one-and two-sample T2 tests. J. Am. Stat. Assoc. 1979; 74: 48-51.
18. Kariya T. A robustness property of Hotelling's T2-test. Ann. Stat. 1981; 9: 211-214.
19. Yuan K, Bentler PM. F-tests for mean and covariance structure analysis. J. Educ. Behav. Stat. 1999; 24: 225-243.
20. Brereton RG. Chemometrics: Data Analysis for the Laboratory and Chemical Plant. Wiley: Chichester, 2003.
21. Grubbs FE. Procedures for detecting outlying observations in samples. Technometrics 1969; 11: 1-21.
22. Daszykowski M, Kaczmarek K, Vander Heyden Y, Walczak B. Robust statistics in data analysis - a review: basic concepts. Chemom. Intell. Lab. Syst. 2007; 85: 203-219.
23. Penny KI, Jolliffe IT. A comparison of multivariate outlier detection methods for clinical laboratory safety data. Statistician 2001; 50: 295-308.