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Volumn 6, Issue , 2005, Pages

Sources of variation in Affymetrix microarray experiments

Author keywords

[No Author keywords available]

Indexed keywords

AFFYMETRIX MICROARRAYS; BIOLOGICAL VARIATION; GENERAL LINEAR MODELING; IMAGE PROCESSING ALGORITHM; MICROARRAY EXPERIMENTS; OPTIMAL EXPERIMENTAL DESIGNS; PEARSON CORRELATION; SOURCES OF VARIATION;

EID: 25444496949     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-214     Document Type: Article
Times cited : (94)

References (39)
  • 1
    • 4043119775 scopus 로고    scopus 로고
    • Applications of biochips: From diagnostics to personalized medicine
    • Jain KK: Applications of biochips: from diagnostics to personalized medicine. Curr Opin Drug Discov Devel 2004, 7(3):285-289.
    • (2004) Curr. Opin. Drug Discov. Devel. , vol.7 , Issue.3 , pp. 285-289
    • Jain, K.K.1
  • 2
    • 0037974525 scopus 로고    scopus 로고
    • Application of microarray technology in environmental and comparative physiology
    • Gracey AY, Cossins AR: Application of microarray technology in environmental and comparative physiology. Annu Rev Physiol 2003, 65:231-259.
    • (2003) Annu. Rev. Physiol. , vol.65 , pp. 231-259
    • Gracey, A.Y.1    Cossins, A.R.2
  • 3
    • 0034927555 scopus 로고    scopus 로고
    • Analysis of variance for gene expression microarray data
    • Kerr MK, Martin M, Churchill GA: Analysis of variance for gene expression microarray data. J Comput Biol 2000, 7(6):819-837.
    • (2000) J. Comput. Biol. , vol.7 , Issue.6 , pp. 819-837
    • Kerr, M.K.1    Martin, M.2    Churchill, G.A.3
  • 4
    • 0036900895 scopus 로고    scopus 로고
    • Fundamentals of experimental design for cDNA microarrays
    • Churchill GA: Fundamentals of experimental design for cDNA microarrays. Nat Genet 2002, Suppl 32:490-495.
    • (2002) Nat. Genet. , Issue.SUPPL. 32 , pp. 490-495
    • Churchill, G.A.1
  • 5
    • 0036319960 scopus 로고    scopus 로고
    • Design issues for cDNA microarray experiments
    • Yang YH, Speed T: Design issues for cDNA microarray experiments. Nat Rev Genet 2002, 3(8):579-88.
    • (2002) Nat. Rev. Genet. , vol.3 , Issue.8 , pp. 579-588
    • Yang, Y.H.1    Speed, T.2
  • 6
    • 0000884487 scopus 로고    scopus 로고
    • Experimental design for gene expression microarrays
    • Kerr MK, Churchill GA: Experimental design for gene expression microarrays. Biostatistics 2001, 2(2):183-201.
    • (2001) Biostatistics , vol.2 , Issue.2 , pp. 183-201
    • Kerr, M.K.1    Churchill, G.A.2
  • 7
    • 0142151385 scopus 로고    scopus 로고
    • Overcoming technical variation and biological variation in quantitative proteomics
    • Molloy MP, Brzezinski EE, Hang J, McDowell MT, VanBogelen RA: Overcoming technical variation and biological variation in quantitative proteomics. Proteomics 2003, 3(10):1912-1919.
    • (2003) Proteomics , vol.3 , Issue.10 , pp. 1912-1919
    • Molloy, M.P.1    Brzezinski, E.E.2    Hang, J.3    McDowell, M.T.4    VanBogelen, R.A.5
  • 8
    • 0036793353 scopus 로고    scopus 로고
    • Assessing sources of variability in microarray gene expression data
    • Spruill SE, Lu J, Hardy S, Weir B: Assessing sources of variability in microarray gene expression data. BioTechniques 2002, 33:916-923.
    • (2002) BioTechniques , vol.33 , pp. 916-923
    • Spruill, S.E.1    Lu, J.2    Hardy, S.3    Weir, B.4
  • 10
    • 0036789519 scopus 로고    scopus 로고
    • Variation in gene expression within and among natural populations
    • Oleksiak MF, Churchill GA, Crawford DL: Variation in gene expression within and among natural populations. Nat Genet 2002, 32(2):261-266.
    • (2002) Nat. Genet. , vol.32 , Issue.2 , pp. 261-266
    • Oleksiak, M.F.1    Churchill, G.A.2    Crawford, D.L.3
  • 11
    • 0842331389 scopus 로고    scopus 로고
    • Quantification of sources of variation and accuracy of sequence discrimination in a replicated microarray experiment
    • Brown JS, Kuhn D, Wisser R, Power E, Schnell R: Quantification of sources of variation and accuracy of sequence discrimination in a replicated microarray experiment. BioTechniques 2004, 36:324-332.
    • (2004) BioTechniques , vol.36 , pp. 324-332
    • Brown, J.S.1    Kuhn, D.2    Wisser, R.3    Power, E.4    Schnell, R.5
  • 12
    • 2942576225 scopus 로고    scopus 로고
    • Sources of variability and effect of experimental approach on expression profiling data interpretation
    • Bakay M, Chen YW, Borup R, Zhao P, Nagaraju K, Hoffman EP: Sources of variability and effect of experimental approach on expression profiling data interpretation. BMC Bioinformatics 2002, 3(1):4.
    • (2002) BMC Bioinformatics , vol.3 , Issue.1 , pp. 4
    • Bakay, M.1    Chen, Y.W.2    Borup, R.3    Zhao, P.4    Nagaraju, K.5    Hoffman, E.P.6
  • 14
    • 1842680967 scopus 로고    scopus 로고
    • Reproducibility, sources of variability, pooling, and sample size: Important considerations for the design of high-density oligonucleotide array experiments
    • Han ES, Wu Y, McCarter R, Nelson JF, Richardson A, Hilsenbeck SG: Reproducibility, sources of variability, pooling, and sample size: important considerations for the design of high-density oligonucleotide array experiments. J Gerontol A Biol Sci Med Sci 2004, 59(4):306-315.
    • (2004) J. Gerontol. A Biol. Sci. Med. Sci. , vol.59 , Issue.4 , pp. 306-315
    • Han, E.S.1    Wu, Y.2    McCarter, R.3    Nelson, J.F.4    Richardson, A.5    Hilsenbeck, S.G.6
  • 15
    • 3042683137 scopus 로고    scopus 로고
    • Hybridization buffer systems impact the quality of filter array data
    • Liu J, Walker N, Waalkes MP: Hybridization buffer systems impact the quality of filter array data. J Pharmacol Toxicol Methods 2004, 50(1):67-71.
    • (2004) J. Pharmacol. Toxicol. Methods , vol.50 , Issue.1 , pp. 67-71
    • Liu, J.1    Walker, N.2    Waalkes, M.P.3
  • 16
    • 0242496185 scopus 로고    scopus 로고
    • A design and statistical perspective on microarray gene expression studies in nutrition: The need for playful creativity and scientific hard-mindedness
    • Page GP, Edwards JW, Barnes S, Weindruch R, Allison DB: A design and statistical perspective on microarray gene expression studies in nutrition: the need for playful creativity and scientific hard-mindedness. Nutrition 2003, 19(11-12):997-1000.
    • (2003) Nutrition , vol.19 , Issue.11-12 , pp. 997-1000
    • Page, G.P.1    Edwards, J.W.2    Barnes, S.3    Weindruch, R.4    Allison, D.B.5
  • 18
    • 0141939435 scopus 로고    scopus 로고
    • The efficiency of pooling mRNA in microarray experiments
    • Kendziorski CM, Zhang Y, Lan H, Attie AD: The efficiency of pooling mRNA in microarray experiments. Biostatistics 2003, 4(3):465-477.
    • (2003) Biostatistics , vol.4 , Issue.3 , pp. 465-477
    • Kendziorski, C.M.1    Zhang, Y.2    Lan, H.3    Attie, A.D.4
  • 21
    • 0035793042 scopus 로고    scopus 로고
    • Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
    • Li C, Wong WH: Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci 2001, 98:31-36.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 31-36
    • Li, C.1    Wong, W.H.2
  • 22
    • 0036947892 scopus 로고    scopus 로고
    • Robust estimators for expression analysis
    • Hubbell E, Liu W, Mei R: Robust estimators for expression analysis. Bioinformatics 2002, 12:1585-92.
    • (2002) Bioinformatics , vol.12 , pp. 1585-1592
    • Hubbell, E.1    Liu, W.2    Mei, R.3
  • 24
    • 2442601878 scopus 로고    scopus 로고
    • A model based background adjustment for oligonucleotide expression arrays
    • Technical Report, John Hopkins University, Department of Biostatistics Working Papers, Baltimore, MD
    • Wu Z, Irizarry R, Gentleman R, Murillo F, Spencer F: A model based background adjustment for oligonucleotide expression arrays. Technical Report, John Hopkins University, Department of Biostatistics Working Papers, Baltimore, MD 2004.
    • (2004)
    • Wu, Z.1    Irizarry, R.2    Gentleman, R.3    Murillo, F.4    Spencer, F.5
  • 26
    • 24144445705 scopus 로고    scopus 로고
    • Improved statistical tests for differential gene expression by shrinking variance components estimates
    • Cui X, Hwang JT, Qiu J, Blades NJ, Churchill GA: Improved statistical tests for differential gene expression by shrinking variance components estimates. Biostatistics 2005, 6(1):59-75.
    • (2005) Biostatistics , vol.6 , Issue.1 , pp. 59-75
    • Cui, X.1    Hwang, J.T.2    Qiu, J.3    Blades, N.J.4    Churchill, G.A.5
  • 28
    • 17844379157 scopus 로고    scopus 로고
    • A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms
    • Woo Y, Affourtit J, Daigle S, Viale A, Johnson K, Naggert J, Churchill G: A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms. J Biomol Tech 2004, 15(4):276-284.
    • (2004) J. Biomol. Tech. , vol.15 , Issue.4 , pp. 276-284
    • Woo, Y.1    Affourtit, J.2    Daigle, S.3    Viale, A.4    Johnson, K.5    Naggert, J.6    Churchill, G.7
  • 29
    • 23844483247 scopus 로고    scopus 로고
    • A study of inter-lab and inter-platform agreement of DNA microarray data
    • Wang H, He X, Band M, Wilson C, Liu L: A study of inter-lab and inter-platform agreement of DNA microarray data. BMC Genomics 2005, 6(1):71.
    • (2005) BMC Genomics , vol.6 , Issue.1 , pp. 71
    • Wang, H.1    He, X.2    Band, M.3    Wilson, C.4    Liu, L.5
  • 31
    • 0043089918 scopus 로고    scopus 로고
    • Transformation and normalization of oligonucleotide microarray data
    • Geller SC, Gregg JP, Hagerman P, Rocke DM: Transformation and normalization of oligonucleotide microarray data. Bioinformatics 2003, 19(14):1817-1823.
    • (2003) Bioinformatics , vol.19 , Issue.14 , pp. 1817-1823
    • Geller, S.C.1    Gregg, J.P.2    Hagerman, P.3    Rocke, D.M.4
  • 32
    • 13244299122 scopus 로고    scopus 로고
    • Comparing transformation methods for DNA microarray data
    • Thygesen HH, Zwinderman AH. Comparing transformation methods for DNA microarray data. BMC Bioinformatics 2004, 5(1):77.
    • (2004) BMC Bioinformatics , vol.5 , Issue.1 , pp. 77
    • Thygesen, H.H.1    Zwinderman, A.H.2
  • 33
    • 9144268360 scopus 로고    scopus 로고
    • Contributing Members of the Toxicogenomics Research Consortium: Empirical evaluation of data transformations and ranking statistics for microarray analysis
    • Qin LX, Kerr KF; Contributing Members of the Toxicogenomics Research Consortium: Empirical evaluation of data transformations and ranking statistics for microarray analysis. Nucleic Acids Res 2004, 32(18):5471-5479.
    • (2004) Nucleic Acids Res. , vol.32 , Issue.18 , pp. 5471-5479
    • Qin, L.X.1    Kerr, K.F.2
  • 34
    • 18844447998 scopus 로고    scopus 로고
    • Statistical development and evaluation of microarray gene expression data filters
    • Pounds S, Cheng C: Statistical development and evaluation of microarray gene expression data filters. J Comput Biol 2005,12(4):482-495.
    • (2005) J. Comput. Biol. , vol.12 , Issue.4 , pp. 482-495
    • Pounds, S.1    Cheng, C.2
  • 35
    • 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, 19:2.
    • (2003) Bioinformatics , vol.19 , pp. 2
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 36
    • 18244389201 scopus 로고    scopus 로고
    • Standardizing global gene expression analysis between laboratories and across platforms
    • Toxicogenomics Research Consortium
    • Toxicogenomics Research Consortium: Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods 2005, 2(5):351-356.
    • (2005) Nat. Methods , vol.2 , Issue.5 , pp. 351-356
  • 39
    • 0030305457 scopus 로고    scopus 로고
    • A language for data analysis and graphics
    • Ihaka R, Gentleman R: A language for data analysis and graphics. J Comp Graph Stat 1996, 5(3):299-314.
    • (1996) J. Comp. Graph. Stat. , vol.5 , Issue.3 , pp. 299-314
    • Ihaka, R.1    Gentleman, R.2


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