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Volumn 8, Issue , 2007, Pages

Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips

Author keywords

[No Author keywords available]

Indexed keywords

BACKGROUND SUBTRACTION; CALIBRATION UNCERTAINTY; FALSE POSITIVE; LARGE AMOUNTS; MICROARRAY EXPERIMENTS; NORMALISATION; POPULAR PLATFORM; TRANSCRIPTOMES;

EID: 34347400362     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-195     Document Type: Article
Times cited : (18)

References (31)
  • 1
    • 0036898577 scopus 로고    scopus 로고
    • Microarray data normalisation and transformation
    • 12454644 10.1038/ng1032
    • Quackenbush J Microarray data normalisation and transformation Nature Genetics 2002 32 496-501 12454644 10.1038/ng1032
    • (2002) Nature Genetics , vol.32 , pp. 496-501
    • Quackenbush, J.1
  • 2
    • 33645326509 scopus 로고    scopus 로고
    • Comparison of Affymetrix GeneChip expression measures
    • 16410320 10.1093/bioinformatics/btk046
    • Irizarry R Wu Z Jaffee H Comparison of Affymetrix GeneChip expression measures Bioinformatics 2006 22 789 16410320 10.1093/bioinformatics/ btk046
    • (2006) Bioinformatics , vol.22 , pp. 789
    • Irizarry, R.1    Wu, Z.2    Jaffee, H.3
  • 3
    • 2342439256 scopus 로고    scopus 로고
    • Comparative analysis of algorithms for signal quantification from oligonucleotide microarrays
    • 10.1093/bioinformatics/btg487 14751998
    • Barash Y Dehan E Krupsky M Franklin W Geraci M Friedman N Kamiski N Comparative analysis of algorithms for signal quantification from oligonucleotide microarrays Bioinformatics 2004 20 6 839-846 10.1093/ bioinformatics/btg487 14751998
    • (2004) Bioinformatics , vol.20 , Issue.6 , pp. 839-846
    • Barash, Y.1    Dehan, E.2    Krupsky, M.3    Franklin, W.4    Geraci, M.5    Friedman, N.6    Kamiski, N.7
  • 4
    • 33748809521 scopus 로고    scopus 로고
    • Probe set algorithms: Is there a rational best bet?
    • 1569879 16942624 10.1186/1471-2105-7-395
    • Seo J Hoffman E Probe set algorithms: Is there a rational best bet? BMC Bioinformatics 2006 7 395 1569879 16942624 10.1186/1471-2105-7-395
    • (2006) BMC Bioinformatics , vol.7 , pp. 395
    • Seo, J.1    Hoffman, E.2
  • 5
    • 0037076772 scopus 로고    scopus 로고
    • Profound effects of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis
    • research0033 126238 12184807 10.1186/gb-2002-3-7-research0033
    • Hoffmann R Seidl T Dugas M Profound effects of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis Genome Biology 2002 3 7 research0033 126238 12184807 10.1186/gb-2002-3-7-research0033
    • (2002) Genome Biology , vol.3 , Issue.7
    • Hoffmann, R.1    Seidl, T.2    Dugas, M.3
  • 7
    • 34347396264 scopus 로고    scopus 로고
    • "Comparisons of annotation predictions for Affymetrix GeneChips"
    • 10.2165/00822942-200605040-00006 17140270
    • Stalteri M Harrison A "Comparisons of annotation predictions for Affymetrix GeneChips" Applied Bioinformatics 2006 5 4 237 10.2165/ 00822942-200605040-00006 17140270
    • (2006) Applied Bioinformatics , vol.5 , Issue.4 , pp. 237
    • Stalteri, M.1    Harrison, A.2
  • 8
    • 33846986793 scopus 로고    scopus 로고
    • "Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips"
    • 1784106 17224057 10.1186/1471-2105-8-13
    • Stalteri M Harrison A "Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips" BMC Bioinformatics 2007 8 13 1784106 17224057 10.1186/1471-2105-8-13
    • (2007) BMC Bioinformatics , vol.8 , pp. 13
    • Stalteri, M.1    Harrison, A.2
  • 9
    • 0037069368 scopus 로고    scopus 로고
    • "Gene expression comparison of biopsies from Duchenne muscular dystrophy (DMD) from normal skeletal muscle"
    • 137534 12415109 10.1073/pnas.192571199
    • Haslett J Sanoudou D Kho A Bennett R Greenberg S Kohane I Beggs A Kunkel L "Gene expression comparison of biopsies from Duchenne muscular dystrophy (DMD) from normal skeletal muscle" PNAS 2002 99 15000 137534 12415109 10.1073/pnas.192571199
    • (2002) PNAS , vol.99 , pp. 15000
    • Haslett, J.1    Sanoudou, D.2    Kho, A.3    Bennett, R.4    Greenberg, S.5    Kohane, I.6    Beggs, A.7    Kunkel, L.8
  • 10
    • 0142121516 scopus 로고    scopus 로고
    • "Exploration, normalization and summaries of high density oligonucleotide array probe level data"
    • 10.1093/biostatistics/4.2.249 12925520
    • Irizarry R Hobbs B Collin F Beazer-Barclay Y Antonellis K Scherf U Speed T "Exploration, normalization and summaries of high density oligonucleotide array probe level data" Biostatistics 2003 4 2 249-264 10.1093/biostatistics/4.2.249 12925520
    • (2003) Biostatistics , vol.4 , Issue.2 , pp. 249-264
    • Irizarry, R.1    Hobbs, B.2    Collin, F.3    Beazer-Barclay, Y.4    Antonellis, K.5    Scherf, U.6    Speed, T.7
  • 12
    • 0035793042 scopus 로고    scopus 로고
    • "Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection"
    • 14539 11134512 10.1073/pnas.011404098
    • Li C Wong W "Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection" PNAS 2001 98 31-36 14539 11134512 10.1073/pnas.011404098
    • (2001) PNAS , vol.98 , pp. 31-36
    • Li, C.1    Wong, W.2
  • 13
    • 6944256813 scopus 로고    scopus 로고
    • "Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise"
    • 10.1038/ng1429 15448691
    • Mendell J Sharifi N Meyers J Martinez-Murillo F Dietz H "Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise" Nature Genetics 2004 36 1073 10.1038/ng1429 15448691
    • (2004) Nature Genetics , vol.36 , pp. 1073
    • Mendell, J.1    Sharifi, N.2    Meyers, J.3    Martinez-Murillo, F.4    Dietz, H.5
  • 17
    • 85035214096 scopus 로고    scopus 로고
    • "Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays"
    • 011906
    • Naef F Magnasco M "Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays" Physical Review (E) 2003 68 1 Pt 1 011906
    • (2003) Physical Review (E) , vol.68 , Issue.1 PART 1
    • Naef, F.1    Magnasco, M.2
  • 18
    • 0038729666 scopus 로고    scopus 로고
    • "A model of molecular interactions on short oligonucleotide microarrays"
    • 10.1038/nbt836 12794640
    • Zhang L Miles M Aldape K "A model of molecular interactions on short oligonucleotide microarrays" Nature Biotechnology 2003 21 7 818 10.1038/nbt836 12794640
    • (2003) Nature Biotechnology , vol.21 , Issue.7 , pp. 818
    • Zhang, L.1    Miles, M.2    Aldape, K.3
  • 19
    • 0037388263 scopus 로고    scopus 로고
    • "Absolute mRNA concentrations from sequence specific calibration of oligonucleotide arrays"
    • 152799 12655013 10.1093/nar/gkg283
    • Hekstra D Taussig A Magnasco M Naef F "Absolute mRNA concentrations from sequence specific calibration of oligonucleotide arrays" Nucleic Acids Research 2003 31 7 1962-1968 152799 12655013 10.1093/nar/ gkg283
    • (2003) Nucleic Acids Research , vol.31 , Issue.7 , pp. 1962-1968
    • Hekstra, D.1    Taussig, A.2    Magnasco, M.3    Naef, F.4
  • 20
    • 25444494145 scopus 로고    scopus 로고
    • "Correlation test to assess low-level processing of high-density oligonucleotide microarray data"
    • 1084343 15799785 10.1186/1471-2105-6-80
    • 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 10.1186/ 1471-2105-6-80
    • (2005) BMC Bioinformatics , vol.6 , pp. 80
    • Ploner, A.1    Miller, L.2    Hall, P.3    Bergh, J.4    Pawitan, Y.5
  • 22
    • 34347402919 scopus 로고    scopus 로고
    • Reply to the letter of Klebanov et al
    • MACQ consortium 10.1038/nbt0107-26
    • Shi L MACQ consortium Reply to the letter of Klebanov et al Nature Biotechnology 2007 25 26 10.1038/nbt0107-26
    • (2007) Nature Biotechnology , vol.25 , pp. 26
    • Shi, L.1
  • 24
    • 0035942271 scopus 로고    scopus 로고
    • "Significance analysis of microarrays applied to the ionizing radiation response"
    • 33173 11309499 10.1073/pnas.091062498
    • Tusher V Tibshirani R Chu G "Significance analysis of microarrays applied to the ionizing radiation response" Proc Natl Acad Sci USA 2001 98 5116 33173 11309499 10.1073/pnas.091062498
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 5116
    • Tusher, V.1    Tibshirani, R.2    Chu, G.3
  • 25
    • 84874661101 scopus 로고    scopus 로고
    • "Transcript assignment for Affymetrix GeneChip probe arrays"
    • Affymetrix Inc
    • Affymetrix Inc "Transcript assignment for Affymetrix GeneChip probe arrays" 2004 http://www.affymetrix.com/support/technical/ whitepapers/netaffxannot_whitepaper.pdf
    • (2004)
  • 27
    • 33645756545 scopus 로고    scopus 로고
    • "Bioinformatics and Computational Biology Solutions using R and Bioconductor"
    • Springer
    • Gentleman R Carey V Huber W Irizarry R Dudoit S "Bioinformatics and Computational Biology Solutions using R and Bioconductor" Springer 2005
    • (2005)
    • Gentleman, R.1    Carey, V.2    Huber, W.3    Irizarry, R.4    Dudoit, S.5
  • 28
    • 0037316303 scopus 로고    scopus 로고
    • "A comparison of normalization methods for high density oligonucleotide array data based on bias and variance"
    • 10.1093/bioinformatics/19.2.185 12538238
    • Bolstad B Irizarry R Astrand M Speed T "A comparison of normalization methods for high density oligonucleotide array data based on bias and variance" Bioinformatics 2003 19 2 185-193 10.1093/ bioinformatics/19.2.185 12538238
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 185-193
    • Bolstad, B.1    Irizarry, R.2    Astrand, M.3    Speed, T.4
  • 30
    • 0036356994 scopus 로고    scopus 로고
    • "Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip arrays"
    • research0005.1 0005.10 10.1186/gb-2001-3-1-research0005
    • Chudin E Walker R Kosaka A Wu S Rabert D Chang T Kreder D "Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip arrays" Genome Biology 2001 3 1 research0005.1 0005.10 10.1186/gb-2001-3-1-research0005
    • (2001) Genome Biology , vol.3 , Issue.1
    • Chudin, E.1    Walker, R.2    Kosaka, A.3    Wu, S.4    Rabert, D.5    Chang, T.6    Kreder, D.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.