Normalization of single-channel DNA array data by principal component analysis

Bioinformatics

Volumn 20, Issue 11, 2004, Pages 1772-1784

  Stoyanova, Radka ^a   Querec, Troy D ^a,c   Brown, Truman R ^b   Patriotis, Christos ^a  

^a FOX CHASE CANCER CENTER   (United States)

^b Och Spine at New York Presbyterian Hospitals   (United States)

^c EMORY UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ACUTE GRANULOCYTIC LEUKEMIA; ACUTE LYMPHOBLASTIC LEUKEMIA; ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; DIAGNOSTIC ACCURACY; DNA HYBRIDIZATION; DNA MICROARRAY; EPITHELIUM CELL; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC SCREENING; HOUSEKEEPING GENE; HUMAN; HUMAN CELL; OVARY CELL; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; SENSITIVITY ANALYSIS; STANDARDIZATION;

EID: 4444286925     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth170     Document Type: Article

References (32)

1. Alter,O., Brown,P.O. and Botstein,D. (2000) Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl Acad. Sci., USA, 97, 10101-10106.
2. Alter,O., Brown,P.O. and Botstein,D. (2003) Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms. Proc. Natl Acad. Sci., USA, 100, 3351-3356.
3. Anderson,T.W. (1971) An Introduction to Multivariate Statistical Analysis. Wiley, New York.
4. Bolstad,B.M., Irizarry,R.A., Astrand,M. and Speed,T.P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-193.
5. Bowtell,D.D. (1999) Options available - from start to finish - for obtaining expression data by microarray. Nat. Genet., 21, 25-32.
6. Butte,A.J., Dzau,V.J. and Glueck,S.B. (2001) Further defining housekeeping, or 'maintenance,' genes Focus on 'A compendium of gene expression in normal human tissues'. Physiol. Genomics, 7, 95-96.
7. Debouck,C. and Goodfellow,P.N. (1999) DNA microarrays in drug discovery and development. Nat. Genet., 21, 48-50.
8. Duggan,D.J., Bittner,M., Chen,Y., Meltzer,P. and Trent,J.M. (1999) Expression profiling using cDNA microarrays. Nat. Genet., 21, 10-14.
9. Eisen,M.B. and Brown,P.O. (1999) DNA arrays for analysis of gene expression. Methods Enzymol., 303, 179-205.
10. Golub,T.R., Slonim,D.K., Tamayo,P., Huard,C., Gaasenbeek,M., Mesirov,J.P., Coller,H., Loh,M.L., Downing,J.R., Caligiuri,M.A., Bloomfield,C.D. and Lander,E.S. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science, 286, 531-537.
11. Hartemink,A., Gifford,D., Jaakola,T. and Young,R. (2001) Maximum likelihood estimation of optimal scaling factors for expression array normalization. Proc. SPIE, 4266, 132-140.
12. Hoffmann,R., Seidl,T. and Dugas,M. (2002) Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis. Genome Biol., 3, RESEARCH0033.
13. Kepler,T.B., Crosby,L. and Morgan,K.T. (2002) Normalization and analysis of DNA microarray data by self-consistency and local regression. Genome Biol., 3, RESEARCH0037.
14. Kerr,M.K., Martin,M. and Churchill,G.A. (2000) Analysis of variance for gene expression microarray data. J. Comput. Biol., 7, 819-837.
15. Lander,E.S. (1999) Array of hope. Nat. Genet., 21, 3-4.
16. Li,C. and Wong,W.H. (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl Acad. Sci., USA, 98, 31-36.
17. Misra,J., Schmitt,W., Hwang,D., Hsiao,L.L., Gullans,S. and Stephanopoulos,G. (2002) Interactive exploration of microarray gene expression patterns in a reduced dimensional space. Genome Res., 12, 1112-1120.
18. Moon,R.C., Thompson,H.J., Becci,P.J., Grubbs,C.J., Gander,R.J., Newton,D.L., Smith,J.M., Phillips,S.L., Henderson,W.R., Mullen,L.T., Brown,C.C. and Sporn,M.B. (1979) N-(4-hydroxyphenyl)retinamide, a new retinoid for prevention of breast cancer in the rat. Cancer Res., 39, 1339-1346.
19. Nielsen,T.O., West,R.B., Linn,S.C., Alter,O., Knowling,M.A., O'Connell,J.X., Zhu,S., Fero,M., Sherlock,G., Pollack,J.R. et al. (2002) Molecular characterisation of soft tissue tumours: a gene expression study. Lancet, 359, 1301-1307.
20. Park,T., Yi,S.G., Kang,S.H., Lee,S., Lee,Y.S. and Simon,R. (2003) Evaluation of normalization methods for microarray Data. BMC Bioinformatics, 4, 33.
21. Patriotis,P.C., Querec,T.D., Gruver,B.N., Brown,T.R. and Patriotis,C. (2001) ArrayExplorer, a program in visual basic for robust and accurate filter cDNA array analysis. Biotechniques, 31, 862-872.
22. Peterson,L.E. (2003) Partitioning large-sample microarray-based gene expression profiles using principal components analysis. Comput. Methods Programs Biomed., 70, 107-119.
23. Quackenbush,J. (2001) Computational analysis of microarray data. Nat. Rev. Genet., 2, 418-427.
24. Sapir,M. and Churchill,G.A. (2000). Published: The Jackson Laboratory Poster.
25. Schadt,E.E., Li,C., Ellis,B. and Wong,W.H. (2001) Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J. Cell Biochem. Suppl., 37(suppl.), 120-125.
26. Schadt,E.E., Li,C., Su,C. and Wong,W.H. (2000) Analyzing high-density oligonucleotide gene expression array data. J. Cell Biochem., 80, 192-202.
27. Schuchhardt,J., Beule,D., Malik,A., Wolski,E., Eickhoff,H., Lehrach,H. and Herzel,H. (2000) Normalization strategies for cDNA microarrays. Nucleic Acids Res., 28, E47.
28. Selvey,S., Thompson,E.W., Matthaei,K., Lea,R.A., Irving,M.G. and Griffiths,L.R. (2001) Beta-actin - an unsuitable internal control for RT-PCR. Mol. Cell Probes, 15, 307-311.
29. Stoyanova,R. and Brown,T.R. (2002) NMR spectral quantitation by principal component analysis. III. A generalized procedure for determination of lineshape variations. J. Magn. Reson., 154, 163-175.
30. Tusher,V.G., Tibshirani,R. and Chu,G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci., USA, 98, 5116-5121.
31. Yang,Y.H., Dudoit,S., Luu,P., Lin,D.M., Peng,V., Ngai,J. and Speed,T.P. (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res., 30, e15.
32. Zien,A., Aigner,T., Zimmer,R. and Lengauer,T. (2001) Centralization: a new method for the normalization of gene expression data. Bioinformatics, 17 (Suppl. 1), S323-S331.