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Volumn 11, Issue , 2010, Pages

Error, reproducibility and sensitivity: A pipeline for data processing of Agilent oligonucleotide expression arrays

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL RESEARCH; BIOLOGICAL SAMPLES; BIOLOGICAL VARIABLES; EXPRESSION MICROARRAY; LONG OLIGONUCLEOTIDE; MATHEMATICAL APPROACH; MULTI-DIMENSIONAL SCALING; QUANTITATIVE ESTIMATES;

EID: 77955108892     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-344     Document Type: Article
Times cited : (26)

References (21)
  • 1
    • 33748491517 scopus 로고    scopus 로고
    • The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
    • 10.1038/nbt1239, 16964229
    • Shi L, et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006, 24:1151-1161. 10.1038/nbt1239, 16964229.
    • (2006) Nat Biotechnol , vol.24 , pp. 1151-1161
    • Shi, L.1
  • 2
    • 84888280481 scopus 로고    scopus 로고
    • Agilent Whole Human Genome Expression Arrays
    • Agilent Whole Human Genome Expression Arrays. 2010, http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/wholehumangenomeoligomicroarraykit/pages/default.aspx
    • (2010)
  • 3
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • 10.1093/bioinformatics/19.2.185, 12538238
    • 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. 10.1093/bioinformatics/19.2.185, 12538238.
    • (2003) Bioinformatics , vol.19 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 4
    • 77749291770 scopus 로고    scopus 로고
    • Frozen robust multiarray analysis (fRMA)
    • 10.1093/biostatistics/kxp059, 20097884
    • McCall MN, Bolstad BM, Irizarry RA. Frozen robust multiarray analysis (fRMA). Biostatistics 2010, 11:242-253. 10.1093/biostatistics/kxp059, 20097884.
    • (2010) Biostatistics , vol.11 , pp. 242-253
    • McCall, M.N.1    Bolstad, B.M.2    Irizarry, R.A.3
  • 6
    • 66549099163 scopus 로고    scopus 로고
    • Transcriptional and functional defects of dendritic cells derived from the MUTZ-3 leukaemia line
    • 10.1111/j.1365-2567.2008.03018.x, 2712111, 19538250
    • Rasaiyaah J, Noursadeghi M, Kellam P, Chain B. Transcriptional and functional defects of dendritic cells derived from the MUTZ-3 leukaemia line. Immunology 2009, 127:429-441. 10.1111/j.1365-2567.2008.03018.x, 2712111, 19538250.
    • (2009) Immunology , vol.127 , pp. 429-441
    • Rasaiyaah, J.1    Noursadeghi, M.2    Kellam, P.3    Chain, B.4
  • 7
    • 0012572299 scopus 로고    scopus 로고
    • A variance-stabilizing transformation for gene-expression microarray data
    • Durbin BP, Hardin JS, Hawkins DM, Rocke DM. A variance-stabilizing transformation for gene-expression microarray data. Bioinformatics 2002, 18(Suppl 1):S105-S110.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Durbin, B.P.1    Hardin, J.S.2    Hawkins, D.M.3    Rocke, D.M.4
  • 8
    • 18744432825 scopus 로고    scopus 로고
    • Ranking: a closer look on globalisation methods for normalisation of gene expression arrays
    • 10.1093/nar/30.11.e50, 117212, 12034851
    • Kroll TC, Wolfl S. Ranking: a closer look on globalisation methods for normalisation of gene expression arrays. Nucleic Acids Res 2002, 30:e50. 10.1093/nar/30.11.e50, 117212, 12034851.
    • (2002) Nucleic Acids Res , vol.30
    • Kroll, T.C.1    Wolfl, S.2
  • 9
    • 34250182087 scopus 로고    scopus 로고
    • Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships
    • 10.1186/gb-2007-8-3-r44, 1868928, 17391524
    • Dabney AR, Storey JD. Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships. Genome Biol 2007, 8:R44. 10.1186/gb-2007-8-3-r44, 1868928, 17391524.
    • (2007) Genome Biol , vol.8
    • Dabney, A.R.1    Storey, J.D.2
  • 10
    • 33845413333 scopus 로고    scopus 로고
    • A new approach to intensity-dependent normalization of two-channel microarrays
    • 10.1093/biostatistics/kxj038, 16636140
    • Dabney AR, Storey JD. A new approach to intensity-dependent normalization of two-channel microarrays. Biostatistics 2007, 8:128-139. 10.1093/biostatistics/kxj038, 16636140.
    • (2007) Biostatistics , vol.8 , pp. 128-139
    • Dabney, A.R.1    Storey, J.D.2
  • 11
    • 34548761943 scopus 로고    scopus 로고
    • Selection and validation of normalization methods for c-DNA microarrays using within-array replications
    • 10.1093/bioinformatics/btm361, 17660210
    • Fan J, Niu Y. Selection and validation of normalization methods for c-DNA microarrays using within-array replications. Bioinformatics 2007, 23:2391-2398. 10.1093/bioinformatics/btm361, 17660210.
    • (2007) Bioinformatics , vol.23 , pp. 2391-2398
    • Fan, J.1    Niu, Y.2
  • 12
    • 34247844352 scopus 로고    scopus 로고
    • Systematic approaches for incorporating control spots and data quality information to improve normalization of cDNA microarray data
    • 10.1080/10543400701199544, 17479391
    • Wang D, Zhang CH, Soares MB, Huang J. Systematic approaches for incorporating control spots and data quality information to improve normalization of cDNA microarray data. J Biopharm Stat 2007, 17:415-431. 10.1080/10543400701199544, 17479391.
    • (2007) J Biopharm Stat , vol.17 , pp. 415-431
    • Wang, D.1    Zhang, C.H.2    Soares, M.B.3    Huang, J.4
  • 14
    • 33845432928 scopus 로고    scopus 로고
    • Adjusting batch effects in microarray expression data using empirical Bayes methods
    • 10.1093/biostatistics/kxj037, 16632515
    • Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007, 8:118-127. 10.1093/biostatistics/kxj037, 16632515.
    • (2007) Biostatistics , vol.8 , pp. 118-127
    • Johnson, W.E.1    Li, C.2    Rabinovic, A.3
  • 16
  • 17
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • 10.1038/nature05874, 2212820, 17571346
    • Birney E, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816. 10.1038/nature05874, 2212820, 17571346.
    • (2007) Nature , vol.447 , pp. 799-816
    • Birney, E.1
  • 18
    • 59849123617 scopus 로고    scopus 로고
    • Genome-wide innate immune responses in HIV-1-infected macrophages are preserved despite attenuation of the NF-kappa B activation pathway
    • 2637478, 19109163
    • Noursadeghi M, Tsang J, Miller RF, Straschewski S, Kellam P, Chain BM, Katz DR. Genome-wide innate immune responses in HIV-1-infected macrophages are preserved despite attenuation of the NF-kappa B activation pathway. J Immunol 2009, 182:319-328. 2637478, 19109163.
    • (2009) J Immunol , vol.182 , pp. 319-328
    • Noursadeghi, M.1    Tsang, J.2    Miller, R.F.3    Straschewski, S.4    Kellam, P.5    Chain, B.M.6    Katz, D.R.7
  • 19
    • 66549099163 scopus 로고    scopus 로고
    • Transcriptional and functional defects of dendritic cells derived from the MUTZ-3 leukaemia line
    • 10.1111/j.1365-2567.2008.03018.x, 2712111, 19538250
    • Rasaiyaah J, Noursadeghi M, Kellam P, Chain B. Transcriptional and functional defects of dendritic cells derived from the MUTZ-3 leukaemia line. Immunology 2009, 127:429-441. 10.1111/j.1365-2567.2008.03018.x, 2712111, 19538250.
    • (2009) Immunology , vol.127 , pp. 429-441
    • Rasaiyaah, J.1    Noursadeghi, M.2    Kellam, P.3    Chain, B.4


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