Analysis with respect to instrumental variables for the exploration of microarray data structures

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Baty, Florent ^a   Facompré, Michaël ^a   Wiegand, Jan ^a   Schwager, Joseph ^b   Brutsche, Martin H ^a  

^a UNIVERSITY HOSPITAL BASEL   (Switzerland)

^b DSM NUTRITIONAL PRODUCTS LTD   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

INSTRUMENTAL VARIABLES; MICROARRAY DATA; MULTI VARIATE ANALYSIS; PERIPHERAL BLOOD; SOURCES OF VARIATION;

ANALYSIS OF VARIANCE (ANOVA); EXPERIMENTS; GENE EXPRESSION;

INSTRUMENTS;

ANALYSIS OF VARIANCE; ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; FLUID INTAKE; GENE EXPRESSION; GENETIC VARIABILITY; HUMAN; HUMAN EXPERIMENT; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; MULTIVARIATE ANALYSIS; NORMAL HUMAN; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; ALGORITHM; ARTIFACT; DEVICE FAILURE ANALYSIS; DEVICES; DNA MICROARRAY; EQUIPMENT DESIGN; GENE EXPRESSION PROFILING; GENETIC DATABASE; PROCEDURES; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; STATISTICAL ANALYSIS;

ALGORITHMS; ARTIFACTS; DATA INTERPRETATION, STATISTICAL; DATABASES, GENETIC; EQUIPMENT DESIGN; EQUIPMENT FAILURE ANALYSIS; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY;

EID: 33749598269     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-422     Document Type: Article

References (26)

1. Alter O, Brown PO, Botstein D: Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci USA 2000, 97(18):10101-10106.
2. Fellenberg K, Hauser NC, Brors B, Neutzner A, Hoheisel JD, Vingron M: Correspondence analysis applied to microarray data. Proc Natl Acad Sci USA 2001, 98(19):10781-10786.
3. Ter Braak CJF: Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis. Ecology 1986, 67:1167-1179.
4. Ter Braak CJF: Partial canonical correspondence analysis. In Classification and Related Methods of Data Analysis Edited by: Bock HH. Amsterdam: Elsevier Science Publishers; 1988:551-558.
5. Wollenberg AL: Redundancy analysis: an alternative for canonical analysis. Psychometrika 1977, 42:207-219.
6. Rao CR: The use and interpretation of principal components analysis in applied research. Sankhya Serie A 1964, 26:329-358.
7. Kenkel NC, Derksen DA, Thomas AG, Watson PR: Multivariate analysis in weed science research. Weed Science 2002, 50(3):281-292.
8. Sabatier R, Lebreton JD, Chessel D: Principal component analysis with instrumental variables as a tool for modelling composition data. In Multiway data analysis Edited by: Coppi R, Bolasco S. North-Holland: Elsevier Science Publishers B.V; 1989:341-352.
9. Dolédec S, Chessel D: Rhytmes saisonniers et composantes stationnelles en milieu aquatique. I - Description d'un plan d'observation complet par projection de variables. Acta Oecologica Oecologia Generalis 1987, 8:403-426.
10. Dolédec S, Chessel D: Rythmes saisonniers et composantes stationnelles en milieu aquatique II. Prise en compte et élimination d'effets dans un tableau faunistique. Acta Oecologica Oecologia Generalis 1989, 10:207-232.
11. Dolédec S, Chessel D: Recent developments in linear ordination methods for environmental sciences. Advances in Ecology 1991, 1:133-155.
12. Lebreton JD, Sabatier R, Banco G, Bacou AM: Principal component and correspondence analysis with respect to instrumental variables : an overview of their role in studies of structure-activity and species-environment relationships. In Applied multivariate analysis in SAR and environmental studies Edited by: Devillers J, Karcher J. Dordrecht: Kluwer; 1991:85-114.
13. Culhane AC, Perrière G, Considine EC, Cotter TG, Higgins DG: Between-group analysis of microarray data. Bioinformatics 2002, 18(12):1600-1608.
14. Supplementary information [http://pulmogene.unibas.ch/articles/iv]
15. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4(2):249-264.
16. Culhane AC, Perriere G, Higgins DG: Cross-platform comparison and visualisation of gene expression data using co-inertia analysis. BMC Bioinformatics 2003, 4:59.
17. Dray S, Chessel D, Thioulouse J: Co-inertia analysis and the linking of ecological data tables. Ecology 2003, 84:3078-3089.
18. Makarenkov V, Legendre P: Nonlinear redundancy analysis and canonical correspondence analysis based on polynomial regression. Ecology 2002, 83:1146-1161.
19. Martens H, Martens M: Multivariate analysis of quality. An introduction Chichester, UK: Wiley; 2001.
20. Tan Q, Brusgaard K, Kruse TA, Oakeley E, Hemmings B, Beck-Nielsen H, Hansen L, Gaster M: Correspondence analysis of microarray time-course data in case-control design. J Biomed Inform 2004, 37(5):358-365. [Evaluation Studies].
21. Perelman S, Mazzella MA, Muschietti J, Zhu T, Casal JJ: Finding unexpected patterns in microarray data. Plant Physiol 2003, 133(4):1717-25.
22. R Development Core Team: R: A language and environment for statistical computing R Foundation for Statistical Computing, Vienna, Austria; 2004.
23. Chessel D, Dufour AB, Thioulouse J: The ade4 package - I: One-table methods. R News 2004, 4:5-10.
24. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5(10):R80.
25. The Gene Ontology Consortium: Gene Ontology: tool for the unification of biology. Nature Genet 2000, 25:25-29.
26. Dennis GJ, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA: DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 2003, 4(5):P3.