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Volumn 118, Issue 1, 2008, Pages 29-41

Assessing quality and normalization of microarrays: Case studies using neurological genomic data

Author keywords

Epilepsy; Genomics; Migraine; Molecular biology; Molecular genetics

Indexed keywords

AMINOLEVULINIC ACID; BETA 2 MICROGLOBULIN; BETA ACTIN; BETA TUBULIN; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; PHOSPHOGLYCERATE KINASE; PORPHOBILINOGEN DEAMINASE; RIBOSOME PROTEIN; TATA BINDING PROTEIN; TRANSFERRIN RECEPTOR;

EID: 44949164750     PISSN: 00016314     EISSN: 16000404     Source Type: Journal    
DOI: 10.1111/j.1600-0404.2007.00979.x     Document Type: Article
Times cited : (6)

References (25)
  • 1
    • 0023240324 scopus 로고
    • Are all significant P values created equal? the analogy between diagnostic tests and clinical research
    • Browner WS, Newman TB. Are all significant P values created equal? The analogy between diagnostic tests and clinical research JAMA 1987 257:2459 63.
    • (1987) JAMA , vol.257 , pp. 2459-63
    • Browner, W.S.1    Newman, T.B.2
  • 2
    • 33750964487 scopus 로고    scopus 로고
    • Quality assessment of Affymetrix GeneChip data
    • Heber S, Sick B. Quality assessment of Affymetrix GeneChip data. Omics 2006 10:358 68.
    • (2006) Omics , vol.10 , pp. 358-68
    • Heber, S.1    Sick, B.2
  • 3
    • 34547633095 scopus 로고    scopus 로고
    • Publishing genomewide association studies
    • Drazen JM, Phimister EG. Publishing genomewide association studies. N Engl J Med 2007 357:496.
    • (2007) N Engl J Med , vol.357 , pp. 496
    • Drazen, J.M.1    Phimister, E.G.2
  • 4
    • 1542784649 scopus 로고    scopus 로고
    • Analysis of Data from Viral DNA Microchips
    • Amaratunga D, Cabrera J. Analysis of Data From Viral DNA Microchips. J Am Stat Assoc 2001 96:1161 70.
    • (2001) J Am Stat Assoc , vol.96 , pp. 1161-70
    • Amaratunga, D.1    Cabrera, J.2
  • 5
    • 33845432928 scopus 로고    scopus 로고
    • Adjusting batch effects in microarray expression data using empirical Bayes methods
    • Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007 8:118 27.
    • (2007) Biostatistics , vol.8 , pp. 118-27
    • Johnson, W.E.1    Li, C.2    Rabinovic, A.3
  • 6
    • 33748491517 scopus 로고    scopus 로고
    • The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
    • Shi L, Reid LH, Jones WD et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006 24:1151 61.
    • (2006) Nat Biotechnol , vol.24 , pp. 1151-61
    • Shi, L.1    Reid, L.H.2    Jones, W.D.3
  • 7
    • 33748491718 scopus 로고    scopus 로고
    • Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project
    • Patterson TA, Lobenhofer EK, Fulmer-Smentek SB et al. Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol 2006 24:1140 50.
    • (2006) Nat Biotechnol , vol.24 , pp. 1140-50
    • Patterson, T.A.1    Lobenhofer, E.K.2    Fulmer-Smentek, S.B.3
  • 8
    • 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 59:306 15.
    • (2004) J Gerontol a Biol Sci Med Sci , vol.59 , pp. 306-15
    • Han, E.S.1    Wu, Y.2    McCarter, R.3    Nelson, J.F.4    Richardson, A.5    Hilsenbeck, S.G.6
  • 10
    • 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 USA 2001 98:31 6.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 31-6
    • Li, C.1    Wong, W.H.2
  • 11
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: Open software development for computational biology and bioinformatics
    • Gentleman RC, Carey VJ, Bates DM et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004 5:R80.
    • (2004) Genome Biol , vol.5
    • Gentleman, R.C.1    Carey, V.J.2    Bates, D.M.3
  • 12
    • 2342439256 scopus 로고    scopus 로고
    • Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays
    • Barash Y, Dehan E, Krupsky M et al. Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays. Bioinformatics 2004 20:839 46.
    • (2004) Bioinformatics , vol.20 , pp. 839-46
    • Barash, Y.1    Dehan, E.2    Krupsky, M.3
  • 13
    • 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 19:185 93.
    • (2003) Bioinformatics , vol.19 , pp. 185-93
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 15
    • 1342288026 scopus 로고    scopus 로고
    • Affy - Analysis of Affymetrix GeneChip data at the probe level
    • Gautier L, Cope L, Bolstad BM, Irizarry RA. affy - analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004 20:307 15.
    • (2004) Bioinformatics , vol.20 , pp. 307-15
    • Gautier, L.1    Cope, L.2    Bolstad, B.M.3    Irizarry, R.A.4
  • 20
    • 2942516310 scopus 로고    scopus 로고
    • Sex genes for genomic analysis in human brain: Internal controls for comparison of probe level data extraction
    • Galfalvy HC, Erraji-Benchekroun L, Smyrniotopoulos P et al. Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction. BMC Bioinformatics 2003 4:37.
    • (2003) BMC Bioinformatics , vol.4 , pp. 37
    • Galfalvy, H.C.1    Erraji-Benchekroun, L.2    Smyrniotopoulos, P.3
  • 22
    • 33644872577 scopus 로고    scopus 로고
    • Limma: Linear models for microarray data
    • In: Gentlemen, R., Carey, V., Dudoit, S., Irizarry, R., Huber, W., eds. New York: Springer
    • Smyth GK. Limma: linear models for microarray data. In:Gentlemen R, Carey V, Dudoit S, Irizarry R, Huber W, eds. Bioinformatics and computational biology solutions using R and bioconductor. New York:Springer, 2005 397 420.
    • (2005) Bioinformatics and Computational Biology Solutions Using R and Bioconductor. , pp. 397-420
    • Smyth, G.K.1
  • 23
    • 48249153186 scopus 로고
    • Intraclass correlation: Uses in assessing rater reliability
    • Shrout PE, Fleiss JL. Intraclass correlation: uses in assessing rater reliability. Psychol Bull 1979 86:420 8.
    • (1979) Psychol Bull , vol.86 , pp. 420-8
    • Shrout, P.E.1    Fleiss, J.L.2
  • 25
    • 0034720002 scopus 로고    scopus 로고
    • Comparison of human adult and fetal expression and identification of 535 housekeeping/maintenance genes
    • Warrington JA, Nair A, Mahadevappa M, Tsyganskaya M. Comparison of human adult and fetal expression and identification of 535 housekeeping/maintenance genes. Physiol Genomics 2000 2:143 7.
    • (2000) Physiol Genomics , vol.2 , pp. 143-7
    • Warrington, J.A.1    Nair, A.2    Mahadevappa, M.3    Tsyganskaya, M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.