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Volumn 10, Issue SUPPL. 1, 2009, Pages

Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations

Author keywords

[No Author keywords available]

Indexed keywords

DATA NORMALIZATION METHODS; DATA PREPROCESSING; GENE EXPRESSION DATA; GENE EXPRESSION MICROARRAY TECHNOLOGY; HOUSEKEEPING GENE; HYBRIDIZATION CONDITIONS; NORMALIZATION METHODS; OLIGONUCLEOTIDE MICROARRAY;

EID: 60849113704     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S1-S24     Document Type: Article
Times cited : (39)

References (33)
  • 1
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
    • 12740579
    • Segal E Shapira M Regev A Pe'er D Botstein D Koller D Friedman N Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data Nat Genet 2003, 34:166-76 12740579
    • (2003) Nat Genet , vol.34 , pp. 166-176
    • Segal, E.1    Shapira, M.2    Regev, A.3    Pe'er, D.4    Botstein, D.5    Koller, D.6    Friedman, N.7
  • 2
    • 2442446708 scopus 로고    scopus 로고
    • Genome-wide discovery of transcriptional modules from DNA sequence and gene expression
    • 12855470
    • Segal E Yelensky R Koller D Genome-wide discovery of transcriptional modules from DNA sequence and gene expression Bioinformatics 2003, 19(Suppl 1):i273-282 12855470
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Segal, E.1    Yelensky, R.2    Koller, D.3
  • 3
    • 6944244084 scopus 로고    scopus 로고
    • A module map showing conditional activity of expression modules in cancer
    • 15448693
    • Segal E Friedman N Koller D Regev A A module map showing conditional activity of expression modules in cancer Nat Genet 2004, 36:1090-1098 15448693
    • (2004) Nat Genet , vol.36 , pp. 1090-1098
    • Segal, E.1    Friedman, N.2    Koller, D.3    Regev, A.4
  • 5
    • 20044392672 scopus 로고    scopus 로고
    • Mining for regulatory programs in the cancer transcriptome
    • 15920519
    • Rhodes DR Chinnaiyan A Mining for regulatory programs in the cancer transcriptome Nat Genet 2005, 37:579-583 15920519
    • (2005) Nat Genet , vol.37 , pp. 579-583
    • Rhodes, D.R.1    Chinnaiyan, A.2
  • 7
    • 13244268329 scopus 로고    scopus 로고
    • Combining gene expression data from different generations of oligonucleotide arrays
    • 528726 15504239
    • Hwang KB Kong S Greenberg S Park P Combining gene expression data from different generations of oligonucleotide arrays BMC Bioinformatics 2004, 5:159 528726 15504239
    • (2004) BMC Bioinformatics , vol.5 , pp. 159
    • Hwang, K.B.1    Kong, S.2    Greenberg, S.3    Park, P.4
  • 9
    • 28544440089 scopus 로고    scopus 로고
    • Transformation of expression intensities across generations of Affymetrix microarrays using sequence matching and regression modeling
    • 1258179 16224098
    • Bhattacharya S Mariani TJ Transformation of expression intensities across generations of Affymetrix microarrays using sequence matching and regression modeling Nucleic Acids Res 2005, 33:e157 1258179 16224098
    • (2005) Nucleic Acids Res , vol.33
    • Bhattacharya, S.1    Mariani, T.J.2
  • 13
    • 25444494145 scopus 로고    scopus 로고
    • Correlation test to assess low-level processing of high-density oligonucleotide microarray data
    • 1084343 15799785
    • Ploner A Miller L Hall P Bergh J Pawitan Y Correlation test to assess low-level processing of high-density oligonucleotide microarray data BMC Bioinformatics 2005, 6:80 1084343 15799785
    • (2005) BMC Bioinformatics , vol.6 , pp. 80
    • Ploner, A.1    Miller, L.2    Hall, P.3    Bergh, J.4    Pawitan, Y.5
  • 15
    • 0038692119 scopus 로고    scopus 로고
    • Human housekeeping genes are compact
    • 12850439
    • Eisenberg E Levanon EY Human housekeeping genes are compact Trends Genet 2003, 19:362-365 12850439
    • (2003) Trends Genet , vol.19 , pp. 362-365
    • Eisenberg, E.1    Levanon, E.Y.2
  • 17
    • 84888296551 scopus 로고    scopus 로고
    • GeneSapiens http://www.genesapiens.org
    • GeneSapiens
  • 20
    • 33748809521 scopus 로고    scopus 로고
    • Probe set algorithms: Is there a rational best bet?
    • 1569879 16942624
    • Seo J Hoffman EP Probe set algorithms: Is there a rational best bet? BMC Bioinformatics 2006, 7:395 1569879 16942624
    • (2006) BMC Bioinformatics , vol.7 , pp. 395
    • Seo, J.1    Hoffman, E.P.2
  • 21
    • 34547830867 scopus 로고    scopus 로고
    • Comparative analysis of microarray normalization procedures: Effects on reverse engineering gene networks
    • 17646307
    • Lim WK Wang K Lefebvre C Califano A Comparative analysis of microarray normalization procedures: Effects on reverse engineering gene networks Bioinformatics 2007, 23:i282-288 17646307
    • (2007) Bioinformatics , vol.23
    • Lim, W.K.1    Wang, K.2    Lefebvre, C.3    Califano, A.4
  • 22
    • 22144461265 scopus 로고    scopus 로고
    • Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset
    • 551536 15693945
    • Choe SE Boutros M Michelson AM Church GM Halfon MS Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset Genome Biol 2005, 6:R16 551536 15693945
    • (2005) Genome Biol , vol.6
    • Choe, S.E.1    Boutros, M.2    Michelson, A.M.3    Church, G.M.4    Halfon, M.S.5
  • 23
    • 32644439684 scopus 로고    scopus 로고
    • Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons
    • 1345700 16432259
    • Harr B Schlotterer C Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons Nucleic Acids Res 2006, 34:e8 1345700 16432259
    • (2006) Nucleic Acids Res , vol.34
    • Harr, B.1    Schlotterer, C.2
  • 24
    • 1342294092 scopus 로고    scopus 로고
    • Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation
    • 100354 11842121
    • 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 100354 11842121
    • (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
  • 25
    • 1342322682 scopus 로고    scopus 로고
    • Effects of Herceptin treatment on global gene expression patterns in HER2-amplified and nonamplified breast cancer cell lines
    • 14647448
    • Kauraniemi P Hautaniemi S Autio R Astola J Monni O Elkahloun A Kallioniemi A Effects of Herceptin treatment on global gene expression patterns in HER2-amplified and nonamplified breast cancer cell lines Oncogene 2004, 23:1010-1013 14647448
    • (2004) Oncogene , vol.23 , pp. 1010-1013
    • Kauraniemi, P.1    Hautaniemi, S.2    Autio, R.3    Astola, J.4    Monni, O.5    Elkahloun, A.6    Kallioniemi, A.7
  • 28
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • 12538238
    • Bolstad BM Irizarry R Astrand M Speed T A comparison of normalization methods for high density oligonucleotide array data based on variance and bias Bioinformatics 2003, 19:185-193 12538238
    • (2003) Bioinformatics , vol.19 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.2    Astrand, M.3    Speed, T.4
  • 31
    • 33845432928 scopus 로고    scopus 로고
    • Adjusting batch effects in microarray expression data using empirical Bayes methods
    • 16632515
    • Johnson WE Li C Rabinovic A Adjusting batch effects in microarray expression data using empirical Bayes methods Biostatistics 2007, 8:118-127 16632515
    • (2007) Biostatistics , vol.8 , pp. 118-127
    • Johnson, W.E.1    Li, C.2    Rabinovic, A.3
  • 33
    • 27544449357 scopus 로고    scopus 로고
    • Fusing microarray experiments with multivariate regression
    • 16204093
    • Gilks WR Tom BD Brazma A Fusing microarray experiments with multivariate regression Bioinformatics 2005, 21(Suppl 2):iI137-143 16204093
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Gilks, W.R.1    Tom, B.D.2    Brazma, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.