메뉴 건너뛰기




Volumn 6, Issue , 2005, Pages

Evaluation of normalization methods for cDNA microarray data by k-NN classification

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION ERRORS; INFORMATIVE MEASURES; K-NN CLASSIFICATIONS; LEAVE-ONE-OUT CROSS-VALIDATION (LOOCV); NORMALIZATION METHODS; NORMALIZATION STRATEGIES; STATISTICAL COMPUTING; SYSTEMATIC EVALUATION;

EID: 25444446813     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-191     Document Type: Article
Times cited : (58)

References (50)
  • 1
    • 0031246430 scopus 로고    scopus 로고
    • Ratio-Based Decisions and the Quantitative Analysis of cDNA Microarray Images
    • Chen Y, Dougherty ER, Bittner ML: Ratio-Based Decisions and the Quantitative Analysis of cDNA Microarray Images. Journal of Biomedical Optics 1997, 2:364-374.
    • (1997) Journal of Biomedical Optics , vol.2 , pp. 364-374
    • Chen, Y.1    Dougherty, E.R.2    Bittner, M.L.3
  • 3
    • 9144268360 scopus 로고    scopus 로고
    • Empirical evaluation of data transformations and ranking statistics for microarray analysis
    • Qin LX, Kerr KF: Empirical evaluation of data transformations and ranking statistics for microarray analysis. Nucleic Acids Res 2004, 32:5471-5479.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 5471-5479
    • Qin, L.X.1    Kerr, K.F.2
  • 4
    • 0034869983 scopus 로고    scopus 로고
    • San Jose, California. Edited by: Bittner ML, Chen Y, Dorsel AN and Dougherty ER. SPIE-International Society for Optical Engineering
    • Yang YH, Dudoit S, Luu P, Speed TP: Normalization for cDNA microarray data: ; San Jose, California. Volume 4266. Edited by: Bittner ML, Chen Y, Dorsel AN and Dougherty ER. SPIE-International Society for Optical Engineering; 2001:141-152.
    • (2001) Normalization for CDNA Microarray Data , vol.4266 , pp. 141-152
    • Yang, Y.H.1    Dudoit, S.2    Luu, P.3    Speed, T.P.4
  • 5
    • 0036898577 scopus 로고    scopus 로고
    • Microarray data normalization and transformation
    • Quackenbush J: Microarray data normalization and transformation. Nat Genet 2002, 32 Suppl 2:496-501.
    • (2002) Nat. Genet. , vol.32 , Issue.SUPPL. 2 , pp. 496-501
    • Quackenbush, J.1
  • 6
    • 0038048164 scopus 로고    scopus 로고
    • Statistical issues in microarray data analysis
    • Edited by: Brownstein MJ and Khodursky AB. Totowa, NJ, Humana Press
    • Smyth GK, Yang YH, Speed TP: Statistical issues in microarray data analysis. In Functional Genomics: Methods and Protocols Volume 224. Edited by: Brownstein MJ and Khodursky AB. Totowa, NJ, Humana Press; 2003:111-136.
    • (2003) Functional Genomics: Methods and Protocols , vol.224 , pp. 111-136
    • Smyth, G.K.1    Yang, Y.H.2    Speed, T.P.3
  • 8
    • 17744401429 scopus 로고    scopus 로고
    • Centralization: A new method for the normalization of gene expression data
    • Zien A, Aigner T, Zimmer R, Lengauer T: Centralization: a new method for the normalization of gene expression data. Bioinformatics 2001, 17:323S-331.
    • (2001) Bioinformatics , vol.17
    • Zien, A.1    Aigner, T.2    Zimmer, R.3    Lengauer, T.4
  • 9
    • 18744432825 scopus 로고    scopus 로고
    • Ranking: A closer look on globalisation methods for normalisation of gene expression arrays
    • Kroll TC, Wolfl S: Ranking: a closer look on globalisation methods for normalisation of gene expression arrays. Nucleic Acids Res 2002, 30:e50.
    • (2002) Nucleic Acids Res. , vol.30
    • Kroll, T.C.1    Wolfl, S.2
  • 11
    • 0003812858 scopus 로고    scopus 로고
    • Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments
    • University of California, Berkeley
    • Dudoit S, Yang YH, Callow MJ, Speed TP: Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. , University of California, Berkeley; 2000.
    • (2000)
    • Dudoit, S.1    Yang, Y.H.2    Callow, M.J.3    Speed, T.P.4
  • 12
    • 0242281980 scopus 로고    scopus 로고
    • Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data
    • Edited by: Parmigiani G, Garrett ES, Irizarry RA and Zeger SL. New York, Springer
    • Dudoit S, Yang YH: Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In The Analysis of Gene Expression Data: Methods and Software Edited by: Parmigiani G, Garrett ES, Irizarry RA and Zeger SL. New York, Springer; 2003:73-101.
    • (2003) The Analysis of Gene Expression Data: Methods and Software , pp. 73-101
    • Dudoit, S.1    Yang, Y.H.2
  • 14
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • Bolstad BM, Irizarry RA, Astrand M, Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193.
    • (2003) Bioinformatics , vol.19 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 15
    • 1342294092 scopus 로고    scopus 로고
    • Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation
    • Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30:e15.
    • (2002) Nucleic Acids Res. , vol.30
    • Yang, Y.H.1    Dudoit, S.2    Luu, P.3    Lin, D.M.4    Peng, V.5    Ngai, J.6    Speed, T.P.7
  • 16
    • 0035875553 scopus 로고    scopus 로고
    • Issues in cDNA microarray analysis: Quality filtering, channel normalization, models of variations and assessment of gene effects
    • Tseng GC, Oh MK, Rohlin L, Liao JC, Wong WH: Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res 2001, 29:2549-2557.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 2549-2557
    • Tseng, G.C.1    Oh, M.K.2    Rohlin, L.3    Liao, J.C.4    Wong, W.H.5
  • 18
    • 0037188875 scopus 로고    scopus 로고
    • Normalization and analysis of DNA microarray data by self-consistency and local regression
    • RESEARCH0037
    • Kepler TB, Crosby L, Morgan KT: Normalization and analysis of DNA microarray data by self-consistency and local regression. Genome Biol 2002, 3:RESEARCH0037.
    • (2002) Genome Biol. , vol.3
    • Kepler, T.B.1    Crosby, L.2    Morgan, K.T.3
  • 19
    • 24644444665 scopus 로고    scopus 로고
    • A Semi-linear Model for Normalization and Analysis of cDNA Microarray Data
    • Iowa City, Statistics and Actuarial Science, The University of Iowa
    • Huang J, Kuo HC, Koroleva I, Zhang CH, Soares MB: A Semi-linear Model for Normalization and Analysis of cDNA Microarray Data. Iowa City, Statistics and Actuarial Science, The University of Iowa; 2003.
    • (2003)
    • Huang, J.1    Kuo, H.C.2    Koroleva, I.3    Zhang, C.H.4    Soares, M.B.5
  • 20
    • 0842321044 scopus 로고    scopus 로고
    • Normalization and analysis of cDNA microarrays using within-array replications applied to neuroblastoma cell response to a cytokine
    • Fan J, Tam P, Woude GV, Ren Y: Normalization and analysis of cDNA microarrays using within-array replications applied to neuroblastoma cell response to a cytokine. Proc Natl Acad Sci U S A 2004, 101:1135-1140.
    • (2004) Proc. Natl. Acad. Sci. U. S. A. , vol.101 , pp. 1135-1140
    • Fan, J.1    Tam, P.2    Woude, G.V.3    Ren, Y.4
  • 23
    • 0041592552 scopus 로고    scopus 로고
    • Quantitative quality control in microarray experiments and the application in data filtering, normalization and false positive rate prediction
    • Wang X, Hessner MJ, Wu Y, Pati N, Ghosh S: Quantitative quality control in microarray experiments and the application in data filtering, normalization and false positive rate prediction. Bioinformatics 2003, 19:1341-1347.
    • (2003) Bioinformatics , vol.19 , pp. 1341-1347
    • Wang, X.1    Hessner, M.J.2    Wu, Y.3    Pati, N.4    Ghosh, S.5
  • 25
    • 84885686921 scopus 로고    scopus 로고
    • Bioconductor Expression Assessment Tool for Affymetrix Oligonucleotide Arrays (affycomp)
    • Irizarry R, cope L: Bioconductor Expression Assessment Tool for Affymetrix Oligonucleotide Arrays (affycomp). 2004 [http://www.bioconductor.org].
    • (2004)
    • Irizarry, R.1    Cope, L.2
  • 29
    • 0034016185 scopus 로고    scopus 로고
    • Genome changes and gene expression in human solid tumors
    • Gray JW, Collins C: Genome changes and gene expression in human solid tumors. Carcinogenesis 2000, 21:443-452.
    • (2000) Carcinogenesis , vol.21 , pp. 443-452
    • Gray, J.W.1    Collins, C.2
  • 31
    • 0141639615 scopus 로고    scopus 로고
    • Efficient leave-one-out cross-validation of kernel fisher discriminant classifiers
    • Cawley GC, Talbot NLC: Efficient leave-one-out cross-validation of kernel fisher discriminant classifiers. Pattern Recognition 2003, 36:2585-2592.
    • (2003) Pattern Recognition , vol.36 , pp. 2585-2592
    • Cawley, G.C.1    Talbot, N.L.C.2
  • 36
    • 12244302667 scopus 로고    scopus 로고
    • Efficient Exact k-NN and Nonparametric Classification in High Dimensions
    • Liu T, Moore A, Gray A: Efficient Exact k-NN and Nonparametric Classification in High Dimensions. 2003.
    • (2003)
    • Liu, T.1    Moore, A.2    Gray, A.3
  • 37
    • 1842607847 scopus 로고    scopus 로고
    • R: A language and environment for statistical computing
    • R Foundation for Statistical Computing
    • Team RDC: R: A language and environment for statistical computing. 2004 [http://www.r-project.org]., R Foundation for Statistical Computing
    • (2004)
    • Team, R.D.C.1
  • 38
    • 17744413236 scopus 로고    scopus 로고
    • Model-based analysis of oligonucleotide arrays: Model validation, design issues and standard error application
    • RESEARCH0032
    • Li C, Hung Wong W: Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol 2001, 2:RESEARCH0032.
    • (2001) Genome Biol. , vol.2
    • Li, C.1    Hung Wong, W.2
  • 39
    • 0242291496 scopus 로고    scopus 로고
    • MAANOVA: A software package for the analysis of spotted cDNA microarray experiments
    • Edited by: Parmigiani G, Garrett ES, Irizarry RA and Zeger SL. New York, Springer
    • Wu H, Kerr MK, Cui X, Churchill GA: MAANOVA: a software package for the analysis of spotted cDNA microarray experiments. In The Analysis of Gene Expression Data: Methods and Software Edited by: Parmigiani G, Garrett ES, Irizarry RA and Zeger SL. New York, Springer; 2003:313-341.
    • (2003) The Analysis of Gene Expression Data: Methods and Software , pp. 313-341
    • Wu, H.1    Kerr, M.K.2    Cui, X.3    Churchill, G.A.4
  • 41
    • 84874666698 scopus 로고    scopus 로고
    • Pam: Prediction analysis for microarrays
    • Hastie T, Tibshirani R, Narasimhan B, Chu G: Pam: prediction analysis for microarrays. 2003 [http://cran.us.r-project.org/src/contrib/Descriptions/pamr.html].
    • (2003)
    • Hastie, T.1    Tibshirani, R.2    Narasimhan, B.3    Chu, G.4
  • 42
    • 0035984265 scopus 로고    scopus 로고
    • Deriving quantitative conclusions from microarray expression data
    • Olshen AB, Jain AN: Deriving quantitative conclusions from microarray expression data. Bioinformatics 2002, 18:961-970.
    • (2002) Bioinformatics , vol.18 , pp. 961-970
    • Olshen, A.B.1    Jain, A.N.2
  • 43
    • 0036013001 scopus 로고    scopus 로고
    • A probabilistic nearest neighbour method for statistical pattern recognition
    • Holmes CC, Adams NM: A probabilistic nearest neighbour method for statistical pattern recognition. J Royal Statistical Soc B 2002, 64:295-306.
    • (2002) J. Royal Statistical Soc. B , vol.64 , pp. 295-306
    • Holmes, C.C.1    Adams, N.M.2
  • 45
    • 84885687568 scopus 로고    scopus 로고
    • The class package in the VR bundle
    • Ripley B: The class package in the VR bundle. 2003 [http://cran.us.r-project.org/src/contrib/Descriptions/VR.html].
    • (2003)
    • Ripley, B.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.