Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets
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Published:2016-09-01
Issue:1
Volume:17
Page:
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ISSN:1471-2105
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Container-title:BMC Bioinformatics
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language:en
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Short-container-title:BMC Bioinformatics
Author:
Oytam Yalchin,Sobhanmanesh Fariborz,Duesing Konsta,Bowden Joshua C.,Osmond-McLeod Megan,Ross Jason
Funder
Commonwealth Scientific and Industrial Research Organisation
Publisher
Springer Science and Business Media LLC
Subject
Applied Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Structural Biology
Reference28 articles.
1. Scherer A. Batch effects and noise in microarray experiments: Sources and solutions. Chichester: Wiley; 2009. 2. Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry R a. Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet. 2010;11(10):733–9. 3. Harper KN, Peters BA, Gamble MV. Batch effects and pathway analysis: Two potential perils in cancer studies involving DNA methylation array analysis. Cancer Epidemiol Biomarkers Prev. 2013;22:1052–60. 4. McLendon R, Friedman A, Bigner D, Van Meir EG, Brat DJ, Mastrogianakis GM, Olson JJ, Mikkelsen T, Lehman N, Aldape K, Alfred Yung WK, Bogler O, VandenBerg S, Berger M, Prados M, Muzny D, Morgan M, Scherer S, Sabo A, Nazareth L, Lewis L, Hall O, Zhu Y, Ren Y, Alvi O, Yao J, Hawes A, Jhangiani S, Fowler G, San Lucas A, Kovar C, Cree A, Dinh H, Santibanez J, Joshi V, Gonzalez-Garay ML, Miller CA, Milosavljevic A, Donehower L, Wheeler DA, Gibbs RA, Cibulskis K, Sougnez C, Fennell T, Mahan S, Wilkinson J, Ziaugra L, Onofrio R, Bloom T, Nicol R, Ardlie K, Baldwin J, Gabriel S, Lander ES, Ding L, Fulton RS, McLellan MD, Wallis J, Larson DE, Shi X, Abbott R, Fulton L, Chen K, Koboldt DC, Wendl MC, Meyer R, Tang Y, Lin L, Osborne JR, Dunford-Shore BH, Miner TL, Delehaunty K, Markovic C, Swift G, Courtney W, Pohl C, Abbott S, Hawkins A, Leong S, Haipek C, Schmidt H, Wiechert M, Vickery T, Scott S, Dooling DJ, Chinwalla A, Weinstock GM, Mardis ER, Wilson RK, Getz G, Winckler W, Verhaak RGW, Lawrence MS, O’Kelly M, Robinson J, Alexe G, Beroukhim R, Carter S, Chiang D, Gould J, Gupta S, Korn J, Mermel C, Mesirov J, Monti S, Nguyen H, Parkin M, Reich M, Stransky N, Weir BA, Garraway L, Golub T, Meyerson M, Chin L, Protopopov A, Zhang J, Perna I, Aronson S, Sathiamoorthy N, Ren G, Yao J, Wiedemeyer WR, Kim H, Won Kong S, Xiao Y, Kohane IS, Seidman J, Park PJ, Kucherlapati R, Laird PW, Cope L, Herman JG, Weisenberger DJ, Pan F, Van Den Berg D, Van Neste L, Mi Yi J, Schuebel KE, Baylin SB, Absher DM, Li JZ, Southwick A, Brady S, Aggarwal A, Chung T, Sherlock G, Brooks JD, Myers RM, Spellman PT, Purdom E, Jakkula LR, Lapuk AV, Marr H, Dorton S, Gi Choi Y, Han J, Ray A, Wang V, Durinck S, Robinson M, Wang NJ, Vranizan K, Peng V, Van Name E, Fontenay GV, Ngai J, Conboy JG, Parvin B, Feiler HS, Speed TP, Gray JW, Brennan C, Socci ND, Olshen A, Taylor BS, Lash A, Schultz N, Reva B, Antipin Y, Stukalov A, Gross B, Cerami E, Qing Wang W, Qin L-X, Seshan VE, Villafania L, Cavatore M, Borsu L, Viale A, Gerald W, Sander C, Ladanyi M, Perou CM, Neil Hayes D, Topal MD, Hoadley KA, Qi Y, Balu S, Shi Y, Wu J, Penny R, Bittner M, Shelton T, Lenkiewicz E, Morris S, Beasley D, Sanders S, Kahn A, Sfeir R, Chen J, Nassau D, Feng L, Hickey E, Zhang J, Weinstein JN, Barker A, Gerhard DS, Vockley J, Compton C, Vaught J, Fielding P, Ferguson ML, Schaefer C, Madhavan S, Buetow KH, Collins F, Good P, Guyer M, Ozenberger B, Peterson J, Thomson E. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008;455:1061–8. 5. Gibbs RA, Belmont JW, Hardenbol P, Willis TD, Yu F, Yang H, Ch’ang L-Y, Huang W, Liu B, Shen Y, Tam PK-H, Tsui L-C, Waye MMY, Wong JT-F, Zeng C, Zhang Q, Chee MS, Galver LM, Kruglyak S, Murray SS, Oliphant AR, Montpetit A, Hudson TJ, Chagnon F, Ferretti V, Leboeuf M, Phillips MS, Verner A, Kwok P-Y, Duan S, Lind DL, Miller RD, Rice JP, Saccone NL, Taillon-Miller P, Xiao M, Nakamura Y, Sekine A, Sorimachi K, Tanaka T, Tanaka Y, Tsunoda T, Yoshino E, Bentley DR, Deloukas P, Hunt S, Powell D, Altshuler D, Gabriel SB, Zhang H, Zeng C, Matsuda I, Fukushima Y, Macer DR, Suda E, Rotimi CN, Adebamowo CA, Aniagwu T, Marshall PA, Matthew O, Nkwodimmah C, Royal CDM, Leppert MF, Dixon M, Stein LD, Cunningham F, Kanani A, Thorisson GA, Chakravarti A, Chen PE, Cutler DJ, Kashuk CS, Donnelly P, Marchini J, McVean GAT, Myers SR, Cardon LR, Abecasis GR, Morris A, Weir BS, Mullikin JC, Sherry ST, Feolo M, Altshuler D, Daly MJ, Schaffner SF, Qiu R, Kent A, Dunston GM, Kato K, Niikawa N, Knoppers BM, Foster MW, Clayton EW, Wang VO, Watkin J, Gibbs RA, Belmont JW, Sodergren E, Weinstock GM, Wilson RK, Fulton LL, Rogers J, Birren BW, Han H, Wang H, Godbout M, Wallenburg JC, L’Archevêque P, Bellemare G, Todani K, Fujita T, Tanaka S, Holden AL, Lai EH, Collins FS, Brooks LD, McEwen JE, Guyer MS, Jordan E, Peterson JL, Spiegel J, Sung LM, Zacharia LF, Kennedy K, Dunn MG, Seabrook R, Shillito M, Skene B, Stewart JG, Valle DL, Clayton EW, Jorde LB, Belmont JW, Chakravarti A, Cho MK, Duster T, Foster MW, Jasperse M, Knoppers BM, Kwok P-Y, Licinio J, Long JC, Marshall PA, Ossorio PN, Wang VO, Rotimi CN, Royal CDM, Spallone P, Terry SF, Lander ES, Lai EH, Nickerson DA, Abecasis GR, Altshuler D, Bentley DR, Boehnke M, Cardon LR, Daly MJ, Deloukas P, Douglas JA, Gabriel SB, Hudson RR, Hudson TJ, Kruglyak L, Kwok P-Y, Nakamura Y, Nussbaum RL, Royal CDM, Schaffner SF, Sherry ST, Stein LD, Tanaka T. The International HapMap Project. Nature. 2003;426:789–96.
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