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Volumn 8, Issue 12, 2009, Pages 5451-5464

Robust-linear-model normalization to reduce technical variability in functional protein microarrays

Author keywords

Global normalization; Interarray variability; Intra array variability; Protein arrays; Quantile normalization; Robust linear model normalization

Indexed keywords

ARTICLE; BIOSEPARATION; CONTROLLED STUDY; DNA MICROARRAY; HUMAN; PRIORITY JOURNAL; PROTEIN BLOOD LEVEL; PROTEIN MICROARRAY; ROBUST LINEAR MODEL; SEROLOGY; SIGNAL TRANSDUCTION; STATISTICAL MODEL; TITRIMETRY;

EID: 71549138357     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr900412k     Document Type: Article
Times cited : (63)

References (46)
  • 1
  • 3
    • 0034934774 scopus 로고    scopus 로고
    • Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
    • Lieb, J. D.; Liu, X.; Botstein, D.; Brown, P. O. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 2001, 28 (4), 327-334.
    • (2001) Nat. Genet. , vol.28 , Issue.4 , pp. 327-334
    • Lieb, J.D.1    Liu, X.2    Botstein, D.3    Brown, P.O.4
  • 5
    • 33846051527 scopus 로고    scopus 로고
    • Protein microarray technology
    • Hall, D. A.; Ptacek, J.; Snyder, M. Protein microarray technology. Mech. Ageing Dev. 2007, 128 (1), 161-167.
    • (2007) Mech. Ageing Dev. , vol.128 , Issue.1 , pp. 161-167
    • Hall, D.A.1    Ptacek, J.2    Snyder, M.3
  • 6
  • 7
    • 13444280261 scopus 로고    scopus 로고
    • Protein microarrays as tools for functional proteomics
    • DOI 10.1016/j.cbpa.2004.12.006
    • LaBaer, J.; Ramachandran, N. Protein microarrays as tools for functional proteomics. Curr. Opin. Chem. Biol. 2005, 9 (1), 14-19. (Pubitemid 40208619)
    • (2005) Current Opinion in Chemical Biology , vol.9 , Issue.1 , pp. 14-19
    • Labaer, J.1    Ramachandran, N.2
  • 8
    • 27644552994 scopus 로고    scopus 로고
    • Advances in functional protein microarray technology
    • DOI 10.1111/j.1742-4658.2005.04970.x
    • Bertone, P.; Snyder, M. Advances in functional protein microarray technology. FEBS J. 2005, 272 (21), 5400-5411. (Pubitemid 41579404)
    • (2005) FEBS Journal , vol.272 , Issue.21 , pp. 5400-5411
    • Bertone, P.1    Snyder, M.2
  • 9
    • 0036024680 scopus 로고    scopus 로고
    • Autoantibody profiling for the study and treatment of autoimmune disease
    • DOI 10.1186/ar426
    • Hueber, W.; Utz, P. J.; Steinman, L.; Robinson, W. H. Autoantibody profiling for the study and treatment of autoimmune disease. Arthritis Res. 2002, 4 (5), 290-295. (Pubitemid 34947142)
    • (2002) Arthritis Research , vol.4 , Issue.5 , pp. 290-295
    • Hueber, W.1    Utz, P.J.2    Steinman, L.3    Robinson, W.H.4
  • 11
    • 10944228461 scopus 로고    scopus 로고
    • Global analysis of protein function using protein microarrays
    • DOI 10.1016/j.mad.2004.09.019, PII S0047637404002210, Functional Genomics of Ageing II
    • Smith, M. G.; Jona, G.; Ptacek, J.; Devgan, G.; Zhu, H.; Zhu, X.; Snyder, M. Global analysis of protein function using protein microarrays. Mech. Ageing Dev. 2005, 126 (1), 171-175. (Pubitemid 40018490)
    • (2005) Mechanisms of Ageing and Development , vol.126 , Issue.1 , pp. 171-175
    • Smith, M.G.1    Jona, G.2    Ptacek, J.3    Devgan, G.4    Zhu, H.5    Zhu, X.6    Snyder, M.7
  • 13
    • 0242407063 scopus 로고    scopus 로고
    • Microarrays to characterize protein interactions on a whole-proteome scale
    • DOI 10.1002/pmic.200300610
    • Schweitzer, B.; Predki, P.; Snyder, M. Microarrays to characterize protein interactions on a whole-proteome scale. Proteomics 2003, 3 (11), 2190-2199. (Pubitemid 37420040)
    • (2003) Proteomics , vol.3 , Issue.11 , pp. 2190-2199
    • Schweitzer, B.1    Predki, P.2    Snyder, M.3
  • 15
    • 14844314814 scopus 로고    scopus 로고
    • Identification of Defensin {alpha}6 as a Potential Biomarker in Colon Adenocarcinoma
    • Nam, M. J.; Kee, M. K.; Kuick, R.; Hanash, S. M. Identification of Defensin {alpha}6 as a Potential Biomarker in Colon Adenocarcinoma. J. Biol. Chem. 2005, 280 (9), 8260-8265.
    • (2005) J. Biol. Chem. , vol.280 , Issue.9 , pp. 8260-8265
    • Nam, M.J.1    Kee, M.K.2    Kuick, R.3    Hanash, S.M.4
  • 17
    • 71549156918 scopus 로고    scopus 로고
    • [accessed 2009 May 7] Available from
    • Molecular Devices. GenePix Pro 6.1 [Internet] [accessed 2009 May 7] Available from: http://www.moleculardevices.com/pages/software/gn-genepix-pro. html.
    • GenePix Pro 6.1 [Internet]
  • 19
    • 0342588237 scopus 로고    scopus 로고
    • Imagene: An integrated computer environment for sequence annotation and analysis
    • DOI 10.1093/bioinformatics/15.1.2
    • Medigue, C.; Rechenmann, F.; Danchin, A.; Viari, A. Imagene: an integrated computer environment for sequence annotation and analysis. Bioinformatics 1999, 15 (1), 2-15. (Pubitemid 29101195)
    • (1999) Bioinformatics , vol.15 , Issue.1 , pp. 2-15
    • Medigue, C.1    Rechenmann, F.2    Danchin, A.3    Viari, A.4
  • 20
    • 71549131099 scopus 로고    scopus 로고
    • Imaging Research Inc. [accessed 2009 May 7] Available from
    • Imaging Research Inc. GE Healthcare Life Sciences - ArrayVision" [Internet] [accessed 2009 May 7] Available from: http://www4.gelifesciences.com/ APTRIX/upp01077.nsf/content/microarrays-analysis-arrayvision?OpenDocument.
    • GE Healthcare Life Sciences - ArrayVision" [Internet]
  • 21
    • 71549120491 scopus 로고    scopus 로고
    • [accessed 2009 May 7] Available from
    • Eisen, M. EisenLab [Internet] [accessed 2009 May 7] Available from: http://rana.lbl.gov/EisenSoftware.htm.
    • EisenLab [Internet]
    • Eisen, M.1
  • 22
    • 71549161558 scopus 로고    scopus 로고
    • [accessed 2009 May 7] Available from
    • TM4. Spotfinder [Internet] [accessed 2009 May 7] Available from: http://www.tm4.org/spotfinder.html.
    • Spotfinder [Internet]
  • 25
    • 0034948896 scopus 로고    scopus 로고
    • A Bayesian framework for the analysis of microarray expression data: Regularized t -test and statistical inferences of gene changes
    • Baldi, P.; Long, A. D. A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinformatics 2001, 17 (6), 509-519.
    • (2001) Bioinformatics , vol.17 , Issue.6 , pp. 509-519
    • Baldi, P.1    Long, A.D.2
  • 26
    • 0002251604 scopus 로고    scopus 로고
    • Confocal scanning microscopy in microarray detection
    • Oxford University Press: Oxford, U.K.
    • Schermer, M. Confocal scanning microscopy in microarray detection. In DNA Microarrays - a Practical Approach; Oxford University Press: Oxford, U.K., 1999; pp 17-42.
    • (1999) DNA Microarrays - a Practical Approach , pp. 17-42
    • Schermer, M.1
  • 27
    • 2442704146 scopus 로고    scopus 로고
    • Profound influence of microarray scanner characteristics on gene expression ratios: Analysis and procedure for correction
    • DOI 10.1186/1471-2164-5-10
    • Lyng, H.; Badiee, A.; Svendsrud, D.; Hovig, E.; Myklebost, O.; Stokke, T. Profound influence of microarray scanner characteristics on gene expression ratios: analysis and procedure for correction. BMC Genomics 2004, 5 (1), 10. (Pubitemid 38671589)
    • (2004) BMC Genomics , vol.5 , pp. 10
    • Lyng, H.1    Badiee, A.2    Svendsrud, D.H.3    Hovig, E.4    Myklebost, O.5    Stokke, T.6
  • 28
    • 13244260827 scopus 로고    scopus 로고
    • Calibration and assessment of channel-specific biases in microarray data with extended dynamical range
    • Bengtsson, H.; Jonsson, G.; Vallon-Christersson, J. Calibration and assessment of channel-specific biases in microarray data with extended dynamical range. BMC Bioinf. 2004, 5 (1), 177.
    • (2004) BMC Bioinf. , vol.5 , Issue.1 , pp. 177
    • Bengtsson, H.1    Jonsson, G.2    Vallon-Christersson, J.3
  • 30
    • 0036898577 scopus 로고    scopus 로고
    • Microarray data normalization and transformation
    • Quackenbush, J. Microarray data normalization and transformation. Nat. Genet. 2002, 32, 496-501.
    • (2002) Nat. Genet. , vol.32 , pp. 496-501
    • Quackenbush, J.1
  • 31
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • DOI 10.1093/bioinformatics/19.2.185
    • Bolstad, B.; Irizarry, R.; Astrand, M.; Speed, T. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19 (2), 185-193. (Pubitemid 36181903)
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 34
    • 1342294092 scopus 로고    scopus 로고
    • Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation
    • Yang, Y. H.; Dudoit, S.; Luu, P.; Lin, D. M.; Peng, V.; Ngai, J.; Speed, T. P. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 2002, 30 (4), e15.
    • (2002) Nucleic Acids Res. , vol.30 , Issue.4
    • Yang, Y.H.1    Dudoit, S.2    Luu, P.3    Lin, D.M.4    Peng, V.5    Ngai, J.6    Speed, T.P.7
  • 35
    • 0037188875 scopus 로고    scopus 로고
    • Normalization and analysis of DNA microarray data by self-consistency and local regression
    • Kepler, T.; Crosby, L.; Morgan, K. Normalization and analysis of DNA microarray data by self-consistency and local regression. Genome Biol. 2002, 3 (7), 0037.1-0037.12.
    • (2002) Genome Biol. , vol.3 , Issue.7
    • Kepler, T.1    Crosby, L.2    Morgan, K.3
  • 39
    • 52049113963 scopus 로고    scopus 로고
    • A concentration-dependent analysis method for high density protein microarrays
    • Marina, O.; Biernacki, M. A.; Brusic, V.; Wu, C. J. A concentration-dependent analysis method for high density protein microarrays. J. Proteome Res. 2008, 7 (5), 2059-2068.
    • (2008) J. Proteome Res. , vol.7 , Issue.5 , pp. 2059-2068
    • Marina, O.1    Biernacki, M.A.2    Brusic, V.3    Wu, C.J.4
  • 40
    • 35748932852 scopus 로고    scopus 로고
    • R Development Core Team. Vienna, Austria: R Foundation for Statistical Computing; [accessed 2009 May 7] Available from
    • R Development Core Team. R: A Language and Environment for Statistical Computing [Internet] 2007 Vienna, Austria: R Foundation for Statistical Computing; [accessed 2009 May 7] Available from: http://www.R-project.org.
    • (2007) R: a Language and Environment for Statistical Computing [Internet]
  • 42
    • 33847705714 scopus 로고    scopus 로고
    • ProCAT: A data analysis approach for protein microarrays
    • Zhu, X.; Gerstein, M.; Snyder, M. ProCAT: a data analysis approach for protein microarrays. Genome Biol. 2006, 7 (11), R110.
    • (2006) Genome Biol. , vol.7 , Issue.11
    • Zhu, X.1    Gerstein, M.2    Snyder, M.3
  • 44
    • 33747886203 scopus 로고    scopus 로고
    • Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques
    • DOI 10.1093/bioinformatics/btl162
    • Sundaresh, S.; Doolan, D. L.; Hirst, S.; Mu, Y.; Unal, B.; Davies, D. H.; Felgner, P. L.; Baldi, P. Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques. Bioinformatics 2006, 22 (14), 1760-1766. (Pubitemid 44288339)
    • (2006) Bioinformatics , vol.22 , Issue.14 , pp. 1760-1766
    • Sundaresh, S.1    Doolan, D.L.2    Hirst, S.3    Mu, Y.4    Unal, B.5    Davies, D.H.6    Felgner, P.L.7    Baldi, P.8
  • 46
    • 11244346557 scopus 로고    scopus 로고
    • Variance stabilization applied to microarray data calibration and to the quantification of differential expression
    • Huber, W.; von Heydebreck, A.; Sültmann, H.; Poustka, A.; Vingron, M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 2002, 18 Suppl 1, S96-104. (Pubitemid 41185642)
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Huber, W.1    Von Heydebreck, A.2    Sultmann, H.3    Poustka, A.4    Vingron, M.5


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