메뉴 건너뛰기




Volumn , Issue , 2008, Pages 151-172

Biological interpretation for microarray normalization selection

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84964780033     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter
Times cited : (6)

References (48)
  • 1
    • 0040191763 scopus 로고    scopus 로고
    • Genomic medicine and the future of health care
    • C. Sander, Genomic medicine and the future of health care, Science, 287, 1977–1978, 2000.
    • (2000) Science , vol.287 , pp. 1977-1978
    • Sander, C.1
  • 2
    • 28344454000 scopus 로고    scopus 로고
    • Molecular classification and molecular forecasting of breast cancer: Ready for clinical application?
    • J. D. Brenton, L. A. Carey, A. A. Ahmed, and C. Caldas, Molecular classification and molecular forecasting of breast cancer: Ready for clinical application? Journal of Clinical Oncology, 23, 7350–7360, 2005.
    • (2005) Journal of Clinical Oncology , vol.23 , pp. 7350-7360
    • Brenton, J.D.1    Carey, L.A.2    Ahmed, A.A.3    Caldas, C.4
  • 3
    • 24044482296 scopus 로고    scopus 로고
    • Use of extreme patient samples for outcome prediction from gene expression data
    • H. Liu, J. Li, and L. Wong, Use of extreme patient samples for outcome prediction from gene expression data, Bioinformatics, 21, 3377–3384, 2005.
    • (2005) Bioinformatics , vol.21 , pp. 3377-3384
    • Liu, H.1    Li, J.2    Wong, L.3
  • 8
    • 27644528185 scopus 로고    scopus 로고
    • Cross-platform comparability of micro array technology: Intraplatform consistency and appropriate data analysis procedures are essential
    • L. Shi, W. Tong, H. Fang, U. Scherf, J. Han, R. K. Puri, F. W. Frueh, et al., Cross-platform comparability of micro array technology: Intraplatform consistency and appropriate data analysis procedures are essential, BMC Bioinformatics, 6 Suppl 2, S12, 2005.
    • (2005) BMC Bioinformatics , vol.6 , pp. S12
    • Shi, L.1    Tong, W.2    Fang, H.3    Scherf, U.4    Han, J.5    Puri, R.K.6    Frueh, F.W.7
  • 9
    • 33748491517 scopus 로고    scopus 로고
    • The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements
    • L. Shi, L. H. Reid, W. D. Jones, R. Shippy, J. A. Warrington, S. C. Baker, et al., The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements, Nature Biotechnology, 24, 1151–1161, 2006.
    • (2006) Nature Biotechnology , vol.24 , pp. 1151-1161
    • Shi, L.1    Reid, L.H.2    Jones, W.D.3    Shippy, R.4    Warrington, J.A.5    Baker, S.C.6
  • 10
  • 11
    • 33748508012 scopus 로고    scopus 로고
    • Evaluation of external RNA controls for the assessment of micro array performance
    • W. Tong, A. B. Lucas, R. Shippy, X. Fan, H. Fang, H. Hong, M. S. Orr, et al., Evaluation of external RNA controls for the assessment of micro array performance, Nature Biotechnology, 24, 1132–1139, 2006.
    • (2006) Nature Biotechnology , vol.24 , pp. 1132-1139
    • Tong, W.1    Lucas, A.B.2    Shippy, R.3    Fan, X.4    Fang, H.5    Hong, H.6    Orr, M.S.7
  • 13
    • 0034210280 scopus 로고    scopus 로고
    • Flow cytometry-based minisequencing: A new platform for high-throughput single-nucleotide polymorphism scoring
    • H. Cai, P. S. White, D. Torney, A. Deshpande, Z. Wang, B. Marrone, and J. P. Nolan, Flow cytometry-based minisequencing: A new platform for high-throughput single-nucleotide polymorphism scoring, Genomics, 66, 135–143, 2000.
    • (2000) Genomics , vol.66 , pp. 135-143
    • Cai, H.1    White, P.S.2    Torney, D.3    Deshpande, A.4    Wang, Z.5    Marrone, B.6    Nolan, J.P.7
  • 14
    • 0034060781 scopus 로고    scopus 로고
    • A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension
    • J. Chen, M. A. Iannone, S. Li, J. D. Taylor, P. Rivers, A. J. Nelson, K. A. Slentz-Kes-ler, et al., A microsphere-based assay for multiplexed single nucleotide polymorphism analysis using single base chain extension, Genome Research, 10, 549–557, 2000.
    • (2000) Genome Research , vol.10 , pp. 549-557
    • Chen, J.1    Iannone, M.A.2    Li, S.3    Taylor, J.D.4    Rivers, P.5    Nelson, A.J.6    Slentz-Kes-Ler, K.A.7
  • 15
    • 33645808222 scopus 로고    scopus 로고
    • Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide micro arrays
    • Y. Wang, C. Barbacioru, F. Hyland, W. Xiao, K. L. Hunkapiller, J. Blake, F. Chan, et al., Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide micro arrays, BMC Genomics, 7, 59, 2006.
    • (2006) BMC Genomics , vol.7 , pp. 59
    • Wang, Y.1    Barbacioru, C.2    Hyland, F.3    Xiao, W.4    Hunkapiller, K.L.5    Blake, J.6    Chan, F.7
  • 16
    • 0034352940 scopus 로고    scopus 로고
    • POWER_SAGE: Comparing statistical tests for SAGE experiments
    • M. Z. Man, X. Wang, and Y. Wang, POWER_SAGE: Comparing statistical tests for SAGE experiments, Bioinformatics, 16, 953–959, 2000.
    • (2000) Bioinformatics , vol.16 , pp. 953-959
    • Man, M.Z.1    Wang, X.2    Wang, Y.3
  • 17
    • 33644501814 scopus 로고    scopus 로고
    • Assessment and integration of publicly available SAGE, cDNA microarray, and oligonucleotide micro array expression data for global coexpression analyses
    • O. L. Griffith, E. D. Pleasance, D. L. Fulton, H. Oveisi, M. Ester, A. S. Siddiqui, and S. J. M. Jones, Assessment and integration of publicly available SAGE, cDNA microarray, and oligonucleotide micro array expression data for global coexpression analyses, Genomics, 86, 476–488, 2005.
    • (2005) Genomics , vol.86 , pp. 476-488
    • Griffith, O.L.1    Pleasance, E.D.2    Fulton, D.L.3    Oveisi, H.4    Ester, M.5    Siddiqui, A.S.6    Jones, S.J.M.7
  • 18
    • 0034130561 scopus 로고    scopus 로고
    • Gene expression analysis by massively parallel signature sequencing (MPSS) on micro-bead arrays
    • S. Brenner, M. Johnson, J. Bridgham, G. Golda, D. H. Lloyd, D. Johnson, S. Luo, et al., Gene expression analysis by massively parallel signature sequencing (MPSS) on micro-bead arrays, Nature Biotechnology, 18, 630–634, 2000.
    • (2000) Nature Biotechnology , vol.18 , pp. 630-634
    • Brenner, S.1    Johnson, M.2    Bridgham, J.3    Golda, G.4    Lloyd, D.H.5    Johnson, D.6    Luo, S.7
  • 19
    • 0036468613 scopus 로고    scopus 로고
    • Lab-on-a-chip: Applications in proteomics
    • S. Mouradian, Lab-on-a-chip: Applications in proteomics, Current Opinion Chemical Biology, 6, 51–56, 2002.
    • (2002) Current Opinion Chemical Biology , vol.6 , pp. 51-56
    • Mouradian, S.1
  • 20
    • 2442705296 scopus 로고    scopus 로고
    • Building addressable libraries: The use of electrochemistry for generating reactive Pd(II) reagents at preselected sites in a ChiB
    • E. Tesfu, K. Maurer, S. R. Ragsdale, and K. F. Moeller, Building addressable libraries: The use of electrochemistry for generating reactive Pd(II) reagents at preselected sites in a ChiB, Journal of the American Chemical Society, 126, 6212–6213, 2004.
    • (2004) Journal of the American Chemical Society , vol.126 , pp. 6212-6213
    • Tesfu, E.1    Maurer, K.2    Ragsdale, S.R.3    Moeller, K.F.4
  • 25
    • 25444515422 scopus 로고    scopus 로고
    • Redefinition of Affymetrix probe sets by sequence overlap with cDNA micro array probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements
    • S. L. Carter, A. C. Eklund, B. H. Mecham, I. S. Kohane, and Z. Szallasi, Redefinition of Affymetrix probe sets by sequence overlap with cDNA micro array probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements, BMC Bioinformatics, 6, 107, 2005.
    • (2005) BMC Bioinformatics , vol.6 , pp. 107
    • Carter, S.L.1    Eklund, A.C.2    Mecham, B.H.3    Kohane, I.S.4    Szallasi, Z.5
  • 26
    • 34250872205 scopus 로고    scopus 로고
    • Three methods for optimization of cross-laboratory and cross-platform microarray expression data
    • P. Stafford and M. Brun, Three methods for optimization of cross-laboratory and cross-platform microarray expression data, Nucleic Acids Research, doic10.1093/nar/gkl1133, 2007.
    • (2007) Nucleic Acids Research
    • Stafford, P.1    Brun, M.2
  • 30
    • 0036898577 scopus 로고    scopus 로고
    • Microarray data normalization and transformation
    • J. Quackenbush, Microarray data normalization and transformation, Nature Genetics, 32 Suppl, 496–501, 2002.
    • (2002) Nature Genetics , vol.32 , pp. 496-501
    • Quackenbush, J.1
  • 32
    • 0032903908 scopus 로고    scopus 로고
    • The transcriptional program in the response of human fibroblasts to serum
    • V. R. Iyer, M. B. Eisen, D. T. Ross, G. Schuler, T. Moore, J. C. Lee, J. M. Trent, et al., The transcriptional program in the response of human fibroblasts to serum, Science, 283, 83–87, 1999.
    • (1999) Science , vol.283 , pp. 83-87
    • Iyer, V.R.1    Eisen, M.B.2    Ross, D.T.3    Schuler, G.4    Moore, T.5    Lee, J.C.6    Trent, J.M.7
  • 34
    • 0031246430 scopus 로고    scopus 로고
    • Ratio-based decisions and the quantitative analysis of cDNA microarray images
    • Y. Chen, E. R. Dougherty, and M. L. Bittner, Ratio-based decisions and the quantitative analysis of cDNA microarray images, Journal of Biomedical Optics, 2, 364–374, 1997.
    • (1997) Journal of Biomedical Optics , vol.2 , pp. 364-374
    • Chen, Y.1    Dougherty, E.R.2    Bittner, M.L.3
  • 35
    • 8844283351 scopus 로고    scopus 로고
    • Which is better for cDNA-micro array-based classification: Ratios or direct intensities
    • S. Attoor, E. R. Dougherty, Y. Chen, M. L. Bittner, and J. M. Trent, Which is better for cDNA-micro array-based classification: Ratios or direct intensities? Bioinformatics, 5, 177, 2004.
    • (2004) Bioinformatics , vol.5 , Issue.177
    • Attoor, S.1    Dougherty, E.R.2    Chen, Y.3    Bittner, M.L.4    Trent, J.M.5
  • 37
    • 0036178995 scopus 로고    scopus 로고
    • Control genes and variability: Absence of ubiquitous reference transcripts in diverse mammalian expression studies
    • P. D. Lee, R. Sladek, C. M. Greenwood, and T. J. Hudson, Control genes and variability: Absence of ubiquitous reference transcripts in diverse mammalian expression studies, Genome Research, 12, 292–297, 2002.
    • (2002) Genome Research , vol.12 , pp. 292-297
    • Lee, P.D.1    Sladek, R.2    Greenwood, C.M.3    Hudson, T.J.4
  • 40
    • 33748809521 scopus 로고    scopus 로고
    • Probe set algorithms: Is there a rational best bet?
    • J. Seo and E. P. Hoffman, Probe set algorithms: Is there a rational best bet? BMC Bioinformatics, 7, 395, 2006.
    • (2006) BMC Bioinformatics , vol.7 , pp. 395
    • Seo, J.1    Hoffman, E.P.2
  • 41
    • 33645651236 scopus 로고    scopus 로고
    • How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results
    • F. F. Millenaar, J. Okyere, S. T. May, M. van Zanten, L. A. Voesenek, and A. J. Peeters, How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results, BMC Bioinformatics, 7, 137, 2006.
    • (2006) BMC Bioinformatics , vol.7 , pp. 137
    • Millenaar, F.F.1    Okyere, J.2    May, S.T.3    van Zanten, M.4    Voesenek, L.A.5    Peeters, A.J.6
  • 42
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high-density oligonucleotide array data based on variance and bias
    • B. M. Bolstad, R. A. Irizarry, M. Astrand, and T. P. Speed, A comparison of normalization methods for high-density oligonucleotide array data based on variance and bias, Bioinformatics, 19, 185–193, 2003.
    • (2003) Bioinformatics , vol.19 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 44
    • 0035793042 scopus 로고    scopus 로고
    • Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
    • C. Li and W. H. Wong, Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection, Proceedings of the National Academy of Sciences, USA, 98, 31–36, 2001.
    • (2001) Proceedings of the National Academy of Sciences, USA , vol.98 , pp. 31-36
    • Li, C.1    Wong, W.H.2
  • 47
    • 8844271685 scopus 로고    scopus 로고
    • Faster cyclic loess: Nor-malizating RNA arrays via linear models
    • K. V. Ballman, D. E. Grill, A. L. Oberg, and T. M. Therneau, Faster cyclic loess: Nor-malizating RNA arrays via linear models, Bioinformatics, 20, 2778–2786, 2004.
    • (2004) Bioinformatics , vol.20 , pp. 2778-2786
    • Ballman, K.V.1    Grill, D.E.2    Oberg, A.L.3    Therneau, T.M.4
  • 48
    • 27744505585 scopus 로고    scopus 로고
    • A two-stage normalization method for partially degraded mRNA micro array data
    • L. Y. Liu, N. Wang, J. R. Lupton, N. D. Turner, R. S. Chapkin, and L. A. Davidson, A two-stage normalization method for partially degraded mRNA micro array data, Bioinformatics, 21, 4000–4006, 2005.
    • (2005) Bioinformatics , vol.21 , pp. 4000-4006
    • Liu, L.Y.1    Wang, N.2    Lupton, J.R.3    Turner, N.D.4    Chapkin, R.S.5    Davidson, L.A.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.