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Volumn 3, Issue 1, 2008, Pages

"Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures

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EID: 52649161839     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-3-11     Document Type: Article
Times cited : (18)

References (53)
  • 1
    • 52649084170 scopus 로고    scopus 로고
    • GeneLogic dilution data
    • GeneLogic dilution data http://www.GeneLogic.com/
    • Dilution Data
  • 2
    • 22144461265 scopus 로고    scopus 로고
    • Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset
    • 551536 15693945 10.1186/gb-2005-6-2-r16
    • Choe S Boutros M Michelson A Church G Halfon M Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset Genome Biol 2005, 6(2):R16. 551536 15693945 10.1186/ gb-2005-6-2-r16
    • (2005) Genome Biol , vol.6 , Issue.2
    • Choe, S.1    Boutros, M.2    Michelson, A.3    Church, G.4    Halfon, M.5
  • 3
    • 52649135991 scopus 로고    scopus 로고
    • Affymetrix
    • Affymetrix spiked-in data set http://www.affymetrix.com/support/ technical/sample_data/datasets.affx
    • Spiked-in Data Set
  • 4
    • 52649112095 scopus 로고    scopus 로고
    • "Hook" calibration of GeneChip-microarrays: Theory and algorithm
    • 10.1186/1748-7188-3-12 18759985
    • Binder H Preibisch S "Hook" calibration of GeneChip-microarrays: Theory and algorithm Algorithms for Molecular Biology 2008, 3:12. 10.1186/1748-7188-3-12 18759985
    • (2008) Algorithms for Molecular Biology , vol.3 , pp. 12
    • Binder, H.1    Preibisch, S.2
  • 7
    • 52649126150 scopus 로고    scopus 로고
    • GeneChip Human Genome U133 Arrays
    • Affymetrix
    • Affymetrix GeneChip Human Genome U133 Arrays Data Sheet 2003.
    • (2003) Data Sheet
  • 9
    • 33646402906 scopus 로고    scopus 로고
    • Meta- and Reanalysis of Gene Expression Profiles of Hot and Cold Thyroid Nodules and Papillary Thyroid Carcinoma for Gene Groups
    • 10.1210/jc.2005-1620 16407496
    • Eszlinger M Wiench M Jarzab B Krohn K Beck M Lauter J Gubala E Fujarewicz K Swierniak A Paschke R Meta- and Reanalysis of Gene Expression Profiles of Hot and Cold Thyroid Nodules and Papillary Thyroid Carcinoma for Gene Groups J Clin Endocrinol Metab 2006, 91(5):1934-1942. 10.1210/jc.2005-1620 16407496
    • (2006) J Clin Endocrinol Metab , vol.91 , Issue.5 , pp. 1934-1942
    • Eszlinger, M.1    Wiench, M.2    Jarzab, B.3    Krohn, K.4    Beck, M.5    Lauter, J.6    Gubala, E.7    Fujarewicz, K.8    Swierniak, A.9    Paschke, R.10
  • 10
    • 33746618889 scopus 로고    scopus 로고
    • Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression
    • 1525186 16776839 10.1186/1471-2164-7-153
    • Zhang L Yoder S Enkemann S Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression BMC Genomics 2006, 7(1):153. 1525186 16776839 10.1186/ 1471-2164-7-153
    • (2006) BMC Genomics , vol.7 , Issue.1 , pp. 153
    • Zhang, L.1    Yoder, S.2    Enkemann, S.3
  • 12
    • 52649134324 scopus 로고    scopus 로고
    • GeneChip Yeast Genome 2.0 array
    • Affymetrix
    • Affymetrix GeneChip Yeast Genome 2.0 array Data Sheet 2004.
    • (2004) Data Sheet
  • 13
    • 33750823409 scopus 로고    scopus 로고
    • A rapid genome-scale response of the transcriptional oscillator to perturbation reveals a period-doubling path to phenotypic change
    • 1613231 17043222 10.1073/pnas.0604860103
    • Li CM Klevecz RR A rapid genome-scale response of the transcriptional oscillator to perturbation reveals a period-doubling path to phenotypic change Proc Natl Acad Sci USA 2006, 103(44):16254-16259. 1613231 17043222 10.1073/pnas.0604860103
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.44 , pp. 16254-16259
    • Li, C.M.1    Klevecz, R.R.2
  • 14
    • 23244431990 scopus 로고    scopus 로고
    • Specific and non-specific hybridization of oligonucleotide probes on microarrays
    • 1366534 15834006 10.1529/biophysj.104.055343
    • Binder H Preibisch S Specific and non-specific hybridization of oligonucleotide probes on microarrays Biophys J 2005, 89:337-352. 1366534 15834006 10.1529/biophysj.104.055343
    • (2005) Biophys J , vol.89 , pp. 337-352
    • Binder, H.1    Preibisch, S.2
  • 16
    • 0142121516 scopus 로고    scopus 로고
    • Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    • 10.1093/biostatistics/4.2.249
    • Irizarry RA Hobbs B Collin F Beazer-Barclay YD Antonellis KJ Scherf U Speed TP Exploration, normalization, and summaries of high density oligonucleotide array probe level data Biostat 2003, 4(2):249-264. 10.1093/biostatistics/4.2.249
    • (2003) Biostat , vol.4 , Issue.2 , pp. 249-264
    • Irizarry, R.A.1    Hobbs, B.2    Collin, F.3    Beazer-Barclay, Y.D.4    Antonellis, K.J.5    Scherf, U.6    Speed, T.P.7
  • 17
    • 37649029846 scopus 로고    scopus 로고
    • DNA hybridization to mismatched templates: A chip study
    • 10.1103/PhysRevE.65.040902
    • Naef F Lim DA Patil N Magnasco M DNA hybridization to mismatched templates: A chip study Phys Rev E 2002, 65:4092-4096. 10.1103/ PhysRevE.65.040902
    • (2002) Phys Rev E , vol.65 , pp. 4092-4096
    • Naef, F.1    Lim, D.A.2    Patil, N.3    Magnasco, M.4
  • 18
    • 85035214096 scopus 로고    scopus 로고
    • Solving the riddle of the bright mismatches: Hybridization in oligonucleotide arrays
    • 10.1103/PhysRevE.68.011906
    • Naef F Magnasco MO Solving the riddle of the bright mismatches: hybridization in oligonucleotide arrays Phys Rev E 2003, 68:11906-11910. 10.1103/PhysRevE.68.011906
    • (2003) Phys Rev E , vol.68 , pp. 11906-11910
    • Naef, F.1    Magnasco, M.O.2
  • 19
    • 9944255305 scopus 로고    scopus 로고
    • Interactions in oligonucleotide duplexes upon hybridisation of microarrays
    • 10.1021/jp049592o
    • Binder H Kirsten T Hofacker I Stadler P Loeffler M Interactions in oligonucleotide duplexes upon hybridisation of microarrays J Phys Chem B 2004, 108(46):18015-18025. 10.1021/jp049592o
    • (2004) J Phys Chem B , vol.108 , Issue.46 , pp. 18015-18025
    • Binder, H.1    Kirsten, T.2    Hofacker, I.3    Stadler, P.4    Loeffler, M.5
  • 20
    • 26444432402 scopus 로고    scopus 로고
    • Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays
    • 10.1021/la051231s 16171364
    • Binder H Preibisch S Kirsten T Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays Langmuir 2005, 21:9287-9302. 10.1021/la051231s 16171364
    • (2005) Langmuir , vol.21 , pp. 9287-9302
    • Binder, H.1    Preibisch, S.2    Kirsten, T.3
  • 21
    • 33748491517 scopus 로고    scopus 로고
    • The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
    • MAQC_Consortium 10.1038/nbt1239 16964229
    • MAQC_Consortium The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements Nat Biotechnol 2006 24(9):1151-1161. 10.1038/nbt1239 16964229
    • (2006) Nat Biotechnol , vol.24 , pp. 1151-1161
  • 24
    • 0442321087 scopus 로고    scopus 로고
    • Reproducibility of gene expression across generations of Affymetrix microarrays
    • 165600 12823866 10.1186/1471-2105-4-27
    • Nimgaonkar A Sanoudou D Butte A Haslett J Kunkel L Beggs A Kohane I Reproducibility of gene expression across generations of Affymetrix microarrays BMC Bioinformatics 2003, 4(1):27. 165600 12823866 10.1186/ 1471-2105-4-27
    • (2003) BMC Bioinformatics , vol.4 , Issue.1 , pp. 27
    • Nimgaonkar, A.1    Sanoudou, D.2    Butte, A.3    Haslett, J.4    Kunkel, L.5    Beggs, A.6    Kohane, I.7
  • 25
    • 38649143214 scopus 로고    scopus 로고
    • A comparison of Affymetrix gene expression arrays
    • 2216046 18005448 10.1186/1471-2105-8-449
    • Robinson M Speed T A comparison of Affymetrix gene expression arrays BMC Bioinformatics 2007, 8(1):449. 2216046 18005448 10.1186/1471-2105-8-449
    • (2007) BMC Bioinformatics , vol.8 , Issue.1 , pp. 449
    • Robinson, M.1    Speed, T.2
  • 26
    • 33646182577 scopus 로고    scopus 로고
    • Thermodynamics of competitive surface adsorption on DNA microarrays - Theoretical aspects
    • 10.1088/0953-8984/18/18/S02
    • Binder H Thermodynamics of competitive surface adsorption on DNA microarrays - theoretical aspects J Phys Cond Mat 2006, 18:S491-S523. 10.1088/0953-8984/18/18/S02
    • (2006) J Phys Cond Mat , vol.18
    • Binder, H.1
  • 27
    • 38049134171 scopus 로고    scopus 로고
    • Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays
    • 2180184 17939865 10.1186/1471-2164-8-373
    • Suzuki S Ono N Furusawa C Kashiwagi A Yomo T Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays BMC Genomics 2007, 8(1):373. 2180184 17939865 10.1186/1471-2164-8-373
    • (2007) BMC Genomics , vol.8 , Issue.1 , pp. 373
    • Suzuki, S.1    Ono, N.2    Furusawa, C.3    Kashiwagi, A.4    Yomo, T.5
  • 28
    • 33745787067 scopus 로고    scopus 로고
    • Adsorption models of hybridization and post-hybridization behaviour on oligonucleotide microarrays
    • 10.1088/0953-8984/18/23/024
    • Burden CJ Pittelkow YE Wilson SR Adsorption models of hybridization and post-hybridization behaviour on oligonucleotide microarrays J Phys Cond Mat 2006, 18:5545-5565. 10.1088/0953-8984/18/23/024
    • (2006) J Phys Cond Mat , vol.18 , pp. 5545-5565
    • Burden, C.J.1    Pittelkow, Y.E.2    Wilson, S.R.3
  • 29
    • 42449102216 scopus 로고    scopus 로고
    • Understanding the physics of oligonucleotide microarrays: The Affymetrix spike-in data reanalysed
    • 10.1088/1478-3975/5/1/016004
    • Burden CJ Understanding the physics of oligonucleotide microarrays: The Affymetrix spike-in data reanalysed Physical Biology 2008, 5:016004. 10.1088/1478-3975/5/1/016004
    • (2008) Physical Biology , vol.5 , pp. 016004
    • Burden, C.J.1
  • 31
    • 33847679625 scopus 로고    scopus 로고
    • Improved precision and accuracy for microarrays using updated probe set definitions
    • 1805763 17288599 10.1186/1471-2105-8-48
    • Sandberg R Larsson O Improved precision and accuracy for microarrays using updated probe set definitions BMC Bioinformatics 2007, 8:48. 1805763 17288599 10.1186/1471-2105-8-48
    • (2007) BMC Bioinformatics , vol.8 , pp. 48
    • Sandberg, R.1    Larsson, O.2
  • 32
    • 52649170249 scopus 로고    scopus 로고
    • Modelling background intensity in Affymetrix Genechips
    • preprint q-BIO.bm/arXiv: 0712.3494v
    • Kroll KM Barkema GT Carlon E Modelling background intensity in Affymetrix Genechips preprint 2007 q-BIO.bm/arXiv: 0712.3494v
    • (2007)
    • Kroll, K.M.1    Barkema, G.T.2    Carlon, E.3
  • 33
    • 33144458398 scopus 로고    scopus 로고
    • A proposed metric for assessing the measurement quality of individual microarrays
    • 1373606 16430768 10.1186/1471-2105-7-35
    • Kim K Page G Beasley TM Barnes S Scheirer K Allison D A proposed metric for assessing the measurement quality of individual microarrays BMC Bioinformatics 2006, 7(1):35. 1373606 16430768 10.1186/1471-2105-7-35
    • (2006) BMC Bioinformatics , vol.7 , Issue.1 , pp. 35
    • Kim, K.1    Page, G.2    Beasley, T.M.3    Barnes, S.4    Scheirer, K.5    Allison, D.6
  • 34
    • 47649102969 scopus 로고    scopus 로고
    • Quality assessment for short oligonucleotide microarray data
    • preprint arXiv:0710.0178v2
    • Brettschneider J Collin F Bolstad BM Speed TP Quality assessment for short oligonucleotide microarray data preprint 2008 arXiv:0710.0178v2.
    • (2008)
    • Brettschneider, J.1    Collin, F.2    Bolstad, B.M.3    Speed, T.P.4
  • 35
    • 1542375902 scopus 로고    scopus 로고
    • Amplification protocols introduce systematic but reproducible errors into gene expression studies
    • 15038166
    • Wilson CL Pepper SD Hey Y Miller CJ Amplification protocols introduce systematic but reproducible errors into gene expression studies Biotechniques 2004, 36:498-506. 15038166
    • (2004) Biotechniques , vol.36 , pp. 498-506
    • Wilson, C.L.1    Pepper, S.D.2    Hey, Y.3    Miller, C.J.4
  • 37
    • 23444456437 scopus 로고    scopus 로고
    • Effects of RNA degradation on gene expression analysis of human postmortem tissues
    • 04-3552fje
    • Lee J Hever A Willhite D Zlotnik A Hevezi P Effects of RNA degradation on gene expression analysis of human postmortem tissues FASEB J 2005, 04-3552fje.
    • (2005) FASEB J
    • Lee, J.1    Hever, A.2    Willhite, D.3    Zlotnik, A.4    Hevezi, P.5
  • 38
    • 41049086156 scopus 로고    scopus 로고
    • Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues
    • 2268927 18298816 10.1186/1471-2164-9-91
    • Popova T Mennerich D Weith A Quast K Effect of RNA quality on transcript intensity levels in microarray analysis of human post-mortem brain tissues BMC Genomics 2008, 9:91. 2268927 18298816 10.1186/1471-2164-9-91
    • (2008) BMC Genomics , vol.9 , pp. 91
    • Popova, T.1    Mennerich, D.2    Weith, A.3    Quast, K.4
  • 41
    • 9444231674 scopus 로고    scopus 로고
    • Amplified RNA degradation in T7-amplification methods results in biased microarray hybridizations
    • 280674 14606961 10.1186/1471-2164-4-44
    • Spiess A-N Mueller N Ivell R Amplified RNA degradation in T7-amplification methods results in biased microarray hybridizations BMC Genomics 2003, 4(1):44. 280674 14606961 10.1186/1471-2164-4-44
    • (2003) BMC Genomics , vol.4 , Issue.1 , pp. 44
    • Spiess, A.-N.1    Mueller, N.2    Ivell, R.3
  • 43
    • 33644975004 scopus 로고    scopus 로고
    • RNA integrity and the effect on the real-time qRT-PCR performance
    • 10.1016/j.mam.2005.12.003 16469371
    • Fleige S Pfaffl MW RNA integrity and the effect on the real-time qRT-PCR performance Molecular Aspects of Medicine 2006, 27:126-139. 10.1016/ j.mam.2005.12.003 16469371
    • (2006) Molecular Aspects of Medicine , vol.27 , pp. 126-139
    • Fleige, S.1    Pfaffl, M.W.2
  • 45
    • 33845562634 scopus 로고    scopus 로고
    • Feature-level exploration of a published Affymetrix GeneChip control dataset
    • 1779590 16953902 10.1186/gb-2006-7-8-404
    • Irizarry RA Cope LM Wu Z Feature-level exploration of a published Affymetrix GeneChip control dataset Genome Biol 2006, 7:404. 1779590 16953902 10.1186/gb-2006-7-8-404
    • (2006) Genome Biol , vol.7 , pp. 404
    • Irizarry, R.A.1    Cope, L.M.2    Wu, Z.3
  • 46
    • 52649181526 scopus 로고    scopus 로고
    • Affymetrix Technical Note
    • Affymetrix IVT Labeling Kit TechnicalNote Technical Note 2004:1-8.
    • (2004) IVT Labeling Kit TechnicalNote , pp. 1-8
  • 47
    • 34548546707 scopus 로고    scopus 로고
    • Characterization of mismatch and high-signal intensity probes associated with Affymetrix genechips
    • 10.1093/bioinformatics/btm306 17553856
    • Wang Y Miao Z-H Pommier Y Kawasaki ES Player A Characterization of mismatch and high-signal intensity probes associated with Affymetrix genechips Bioinformatics 2007, 23(16):2088-2095. 10.1093/bioinformatics/ btm306 17553856
    • (2007) Bioinformatics , vol.23 , Issue.16 , pp. 2088-2095
    • Wang, Y.1    Miao, Z.-H.2    Pommier, Y.3    Kawasaki, E.S.4    Player, A.5
  • 48
    • 33744542889 scopus 로고    scopus 로고
    • Relationship between gene expression and observed intensities in DNA microarrays - A modeling study
    • 1472623 16723429 10.1093/nar/gkl122
    • Held GA Grinstein G Tu Y Relationship between gene expression and observed intensities in DNA microarrays - a modeling study Nucl Acids Res 2006, 34:e70. 1472623 16723429 10.1093/nar/gkl122
    • (2006) Nucl Acids Res , vol.34
    • Held, G.A.1    Grinstein, G.2    Tu, Y.3
  • 50
    • 0033921173 scopus 로고    scopus 로고
    • DNA, RNA and hybrid RNA-DNA oligomers of identical sequence: Structural and dynamic differences
    • 10.1016/S0301-4622(00)00157-5 11011698
    • Barone F Cellai L Matzeu F Pedone F DNA, RNA and hybrid RNA-DNA oligomers of identical sequence: Structural and dynamic differences Biophys Chem 2000, 86(1):37-47. 10.1016/S0301-4622(00)00157-5 11011698
    • (2000) Biophys Chem , vol.86 , Issue.1 , pp. 37-47
    • Barone, F.1    Cellai, L.2    Matzeu, F.3    Pedone, F.4
  • 52
    • 0036318088 scopus 로고    scopus 로고
    • Temperature dependence of thermodynamic properties for DNA/DNA and RNA/ DNA duplex formation
    • 10.1046/j.1432-1033.2002.02970.x 12071944
    • Wu P Nakano S Sugimoto N Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation Eur J Biochem 2002, 269(12):2821-2830. 10.1046/j.1432-1033.2002.02970.x 12071944
    • (2002) Eur J Biochem , vol.269 , Issue.12 , pp. 2821-2830
    • Wu, P.1    Nakano, S.2    Sugimoto, N.3


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