Improving the analysis of designed studies by combining statistical modelling with study design information

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Thissen, Uwe ^a,b   Wopereis, Suzan ^a,b   van den Berg, Sjoerd A A ^a,c   Bobeldijk, Ivana ^b   Kleemann, Robert ^b   Kooistra, Teake ^b   van Dijk, Ko Willems ^c   van Ommen, Ben ^a,b   Smilde, Age K ^b,d  

^a TOP INSTITUTE FOOD AND NUTRITION   (Netherlands)

^b TNO   (Netherlands)

^c LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^d UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ANOVA (ANALYSIS OF VARIANCE); BIOLOGICAL INTERPRETATION; COMPLEX BIOLOGICAL SYSTEMS; DATA DECOMPOSITION; INTERVENTION STUDIES; PARTIAL LEAST SQUARE (PLS); STATISTICAL MODELING; STATISTICAL MODELLING;

LEAST SQUARES APPROXIMATIONS; REGRESSION ANALYSIS;

ANALYSIS OF VARIANCE (ANOVA);

ANIMAL; ARTICLE; FACTUAL DATABASE; HUMAN; METABOLOMICS; METHODOLOGY; STATISTICAL MODEL; STATISTICS;

ANIMALS; DATABASES, FACTUAL; HUMANS; METABOLOMICS; MODELS, STATISTICAL;

EID: 62849099705     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-52     Document Type: Article

References (32)

1. Bijlsma S Bobeldijk I Verheij ER Ramaker R Kochhar S Macdonald IA van Ommen B Smilde AK Large-scale human metabolomics studies: A validation strategy for data (pre-)processing and validation Analytical Chemistry 2006, 78:567-574. 10.1021/ac051495j 16408941
2. Wettenhall JM Smyth GK LimmaGUI: A graphical user interface for linear modelling of microarray data Bioinformatics 2004, 20:3705-3706. 10.1093/ bioinformatics/bth449 15297296
3. Fardet A Llorach R Martin J-F Besson C Lyan B Pujos-Guillot E Scalbert A A liquid Chromatography-Quadrupole Time-of-Flight (LC-QTOF)-based Metabolomic Approach Reveals New Metabolic Effects of Catechin in Rats Fed High-Fat Diets J Proteome Res 2008, 7:2388-2398. 10.1021/pr800034h 18484765
4. Hummel M Meister R Mansmann U GlobalANCOVA: Exploration and assessment of gene group effects Bioinformatics 2008, 24:78-85. 10.1093/ bioinformatics/btm531 18024976
5. Smilde AK Jansen JJ Hoefsloot HCJ Lamers R-JAN Greef van der J Timmerman ME ANOVA-Simultaneous Component Analysis (ASCA): A new tool for analyzing designed metabolomics data Bioinformatics 2005, 21:3043-3048. 10.1093/bioinformatics/bti476 15890747
6. Jansen JJ Hoefsloot HCJ Greef van der J Timmerman ME Westerhuis JA Smilde AK ASCA: Analysis of multivariate data obtained from an experimental design Journal of Chemometrics 2005, 19:469-481. 10.1002/ cem.952
7. Harrington PB Vieira NE Espinoza J Nien JK Romero R Yergey AL Analysis of variance-principal component analysis: A soft tool for proteomic discovery Analytica Chimica Acta 2005, 544:118-127. 10.1016/ j.aca.2005.02.042
8. Luthria DL Mukhopadhyay S Robbins RJ Finley JW Banuelos GS Harnly JM UV spectral fingerprinting and analysis of variance-principal component analysis: A useful tool for characterizing sources of variance in plant materials J Agr Food Chem 2008, 56:5457-5462. 10.1021/jf0734572
9. de Noord OE Theobald EH Multilevel component analysis and multilevel PLS of chemical process data Journal of chemometrics 2005, 19:301-307. 10.1002/cem.933
10. Maagdenberg Van den AM Hofker MH Krimpenfort PJ de Bruijn I van Vlijmen B Boom van der H Havekes LM Frants RR Transgenic mice carrying the apolipoprotein E3-Leiden gene exhibit hyperlipoproteinemia J Biol Chem 1993, 268:10540-5. 7683682
11. Müller M Kersten S Nutrigenomics: Goals and strategies Nature Reviews 2003, 4:315-322. 10.1038/nrg1047 12671662
12. Searle SR Linear models John Wiley & Sons, New York First 1971.
13. Ten Berge JMF Kiers HAL Stel van der V Simultaneous Components Analysis Statistica Applicata 1992, 4:377-392.
14. Jackson JE A user's guide to principal components Wiley - Interscience, New York First 1991.
15. Timmerman ME Kiers HAL Four simultaneous component models for the analysis of multivariate time series from more than one subject to model intraindividual and interindividual differences Psychometrica 2003, 86:105-122. 10.1007/BF02296656
16. Martens H Næs T Multivariate calibration Wiley, New York 1989.
17. Boulesteix A-L Strimmer K Partial least squares: A versatile tool for the analysis of high-dimensional genomic data Briefings in bioinformatics 2006, 8:32-44. 10.1093/bib/bbl016 16772269
18. Stone M Cross-validatory choice and assessment of statistical predictions Journal of the royal statistical society. Series B (Methodological) 1974, 36:111-147.
19. Cruciani G Baroni M Costantino G Riganelli D Skagerberg B Predictive Ability of Regression Models. Part I: Standard Deviation of Prediction Errors (SDEP) Journal of Chemometrics 1992, 6:335-346. 10.1002/ cem.1180060604
20. Baroni M Clementi S Cruciani G Costantino G Riganelli D Oberrauch E Predictive Ability of Regression Models. Part II: Selection of the Best Predictive PLS Model Journal of Chemometrics 1992, 6:347-356. 10.1002/ cem.1180060605
21. Smit S van Breemen MJ Hoefsloot HCJ Smilde AK Aerts JMFG de Koster CG Assessing the statistical validity of proteomics based biomarkers Anal Chim Acta 2007, 592:210-217. 10.1016/j.aca.2007.04.043 17512828
22. Westerhuis JA Hoefsloot HCJ Smit S Vis DJ Smilde AK van Velzen EJJ van Duijnhoven JPM van Dorsten FA Assessment of PLSDA crossvalidation Metabolomics 2008, 4:81-89. 10.1007/s11306-007-0099-6
23. Martens H Martens M Modified jack-knife estimation of parameter uncertainty in bilinear modeling by partial least squares regression (PLSR) Food Qual Prefer 2000, 11:5-16. 10.1016/S0950-3293(99)00039-7
24. Faber NM Uncertainty estimation for multivariate regression coefficients Chemometrics and intelligent laboratory systems 2002, 64:169-179. 10.1016/S0169-7439(02)00102-8
25. Kleemann R Princen HMG Emeis JJ Jukema JW Fontijn RD Horrevoets AJG Kooistra T Havekes L Rosuvastin reduces atherosclerosis development beyond and independent of its plasma cholesterol-lowering effect in APOE*3-Leiden transgenic mice: Evidence for anti-inflammatory effects of rosuvastatin Circulation 2003, 108:1368-1374. 10.1161/ 01.CIR.0000086460.55494.AF 12939225
26. Berg van den RA Hoefsloot HCJ Westerhuis JA Smilde AK Werf van der MJ Centering, scaling, and transformations: Improving the biological information content of metabolomics data BMC Genomics 2006, 7:142. 1534033 16762068 10.1186/1471-2164-7-142
27. Fujikoshi Y Two-way ANOVA models with unbalanced data Discrete Mathematics 1993, 116:315-334. 10.1016/0012-365X(93)90410-U
28. Buck SF A method of estimation of missing values in multivariate data suitable for use with an electronic computer J Roy Statist Soci 1960, B22:302-306.
29. Little RJA Rubin DB Statistical analysis with missing data Wiley Series in probability and mathematical statistics, New York 1987.
30. Rubin DB Schenker N Multiple imputation in health-care databases: An overview and some applications Stat Med 1991, 10:585-598. 10.1002/ sim.4780100410 2057657
31. Vis DJ Westerhuis JA Smilde AK Greef van der J Statistical validation of megavariate effects in ASCA BMC Bioinformatics 2007, 8:322. 2211757 17760983 10.1186/1471-2105-8-322
32. Simopoulus AP Omega-3 fatty acids in inflammation and autoimmune diseases Journal of the American College of Nutrition 2002, 21:495-505. 12480795