The comparison of different normalization methods in microarray data

Progress in Biochemistry and Biophysics

Volumn 34, Issue 6, 2007, Pages 625-633

  Tan, Xia Jun ^a   Zhang, Yong Xin ^b   Qian, Min Ping ^a   Zhang, You Yi ^b   Deng, Ming Hua ^a  

^a PEKING UNIVERSITY   (China)

^b PEKING UNIVERSITY THIRD HOSPITAL   (China)

Author keywords

Correlation coefficient; Microarray; Normalization

Indexed keywords

EID: 34548561608     PISSN: 10003282     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (22)

1. Imbeaud S, Auffray C. The 39 steps in gene expression profiling: critical issues and proposed best practices for microarray experiments. Drug Discovery Today, 2005, 10 (17): 1175-1182
2. Allison D B, Cui X Q, Page C P, et al. Microarray data analysis: from disarray to consolidation and consensus. Nature Reviews Genetics, 2006, 7: 55
3. Wilson D L, Buckley M J, Helliwell C A, et al. New normalization methods for cDNA microarray data. Bioinformatics, 2003, 19 (11): 1325-1332
4. Hoffmann R, Seidl R, Dugas M. Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis. Genome Biol, 2002, 3 (7): RESEARCH0033.
5. Lee P D, Sladek R, Greenwood C M T, et al. Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies. Genome Res, 2002, 12 (2): 292-297
6. Yang Y H, Dudoit S, Luu P, et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res, 2002, 30 (4): e15
7. Bolstad B M, Irizarry R A, Astrand M, et al. A comparison of normalization method for high density oligonucleotide array data based on variance and bias. Bioinformatics, 2003, 19 (2): 185-193
8. Workman C, Jensen L J, Jarmer H, et al. A new non-linear normalization methods for reducing variability in DNA microarray experiments. Genome Biol, 2002, 3 (9): research0048
9. Li C, Hung Wong W. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol, 2001, 2 (8): REASERCH0032
10. Park T, Yi S G, Kang S H, et al. Evaluation of normalization methods for microarray data. BMC Bioinformatics, 2003, 4: 33
11. Wu W, Xing E P, Myers C, et al. Evaluation of normalization methods for cDNA microarray data by k-NN classification. BMC Bioinformatics, 2005, 6: 191
12. Qin L X, Kerr D F. Empirical evaluation of data transformations and ranking statistics for microarray analysis. Nucleic Acids Research, 2004, 32(18): 5471-5479
13. Choe S E, Boutros M, Michelson A M, et al. Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol, 2005, 6 (2): R16
14. Ryden P, Andersson H, Landfors M, et al. Evaluation of microarray data normalization procedures using spike-in experiments. BMC Bioinformatics, 2006, 7: 300
15. Segal E, Shapira M, Regev A, et al. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nature Genetics, 2003, 34 (12): 166-176
16. Eisen M B, Spellman P T, Brown P O, et al. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA, 1998, 95 (25): 14863-14868
17. Qiu X, Brooks A I, Klebanov L, et al. The effect of normalization on the correlation structure of microarray data. BMC Bioinformatics, 2005, 6: 120
18. Ploner A. Miller L, Hall P, et al. Correlation test to assess low-level processing of high-density oligonucleotide microarray data. BMC Bioinformatics, 2005, 6: 80
19. Yeoh E J, Ross M E, Shurtleff S A, et al. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by expression profiling. Cancer Cell, 2002, 1 (2): 133-143
20. Irizarry R A, Hobbs B, Collin F, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 2003, 4 (2): 249-264
21. Irizarry R A, Warren D, Spencer F, et al. Multiple-laboratory comparison of microarray platforms. Nature Methods, 2005, 2 (5): 345-350
22. Kim S Y, Lee J W, Bae J S. Effect of data normalization on fuzzy clustering of DNA microarray data. BMC Bioinformatics, 2006, 7: 134