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Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis
Reinhard Hoffmann, Thomas Seidl, Martin Dugas
Genome Biol. 2002; 3(7): research0033.1–research0033.11. Published online 2002 June 14.
PMCID:
PMC126238
Abstract Full Text PDF–4.0M

Is Cited by the Following 22 Articles in this Archive:

A comparison on effects of normalisations in the detection of differentially expressed genes
Monica Chiogna, Maria Sofia Massa, Davide Risso, Chiara Romualdi
BMC Bioinformatics. 2009; 10: 61. Published online 2009 February 13. doi: 10.1186/1471-2105-10-61
PMCID:
PMC2680204
Abstract Full Text PDF–483K Supplementary Material
Methods for evaluating gene expression from Affymetrix microarray datasets
Ning Jiang, Lindsey J Leach, Xiaohua Hu, Elena Potokina, Tianye Jia, Arnis Druka, Robbie Waugh, Michael J Kearsey, Zewei W Luo
BMC Bioinformatics. 2008; 9: 284. Published online 2008 June 17. doi: 10.1186/1471-2105-9-284
PMCID:
PMC2442103
Abstract Full Text PDF–540K Supplementary Material
Genome-wide screen for temperature-regulated genes of the obligate intracellular bacterium, Rickettsia typhi
Sheila M Dreher-Lesnick, Shane M Ceraul, M Sayeedur Rahman, Abdu F Azad
BMC Microbiol. 2008; 8: 61. Published online 2008 April 15. doi: 10.1186/1471-2180-8-61
PMCID:
PMC2335108
Abstract Full Text PDF–417K Supplementary Material
Normalization of oligonucleotide arrays based on the least-variant set of genes
Stefano Calza, Davide Valentini, Yudi Pawitan
BMC Bioinformatics. 2008; 9: 140. Published online 2008 March 5. doi: 10.1186/1471-2105-9-140
PMCID:
PMC2324100
Abstract Full Text PDF–11M Supplementary Material
A new method for class prediction based on signed-rank algorithms applied to Affymetrix® microarray experiments
Thierry Rème, Dirk Hose, John De Vos, Aurélien Vassal, Pierre-Olivier Poulain, Véronique Pantesco, Hartmut Goldschmidt, Bernard Klein
BMC Bioinformatics. 2008; 9: 16. Published online 2008 January 11. doi: 10.1186/1471-2105-9-16
PMCID:
PMC2248160
Abstract Full Text PDF–396K
Different normalization strategies for microarray gene expression traits affect the heritability estimation
Jun Ma, Zhaohui S Qin
BMC Proc. 2007; 1(Suppl 1): S154. Published online 2007 December 18.
PMCID:
PMC2367576
Abstract Full Text PDF–235K
Transcriptional Dysregulation in a Transgenic Model of Parkinson’s Disease
Talene A. Yacoubian, Ippolita Cantuti-Castelvetri, Bérengère Bouzou, Georgios Asteris, Pamela J. McLean, Bradley T. Hyman, David G. Standaert
Neurobiol Dis. Author manuscript; available in PMC 2009 July 9.
Published in final edited form as: Neurobiol Dis. 2008 March; 29(3): 515–528. Published online 2007 November 28. doi: 10.1016/j.nbd.2007.11.008
PMCID:
PMC2707844
Abstract Full Text PDF–1.2M Supplementary Material
Model-based analysis of two-color arrays (MA2C)
Jun S Song, W Evan Johnson, Xiaopeng Zhu, Xinmin Zhang, Wei Li, Arjun K Manrai, Jun S Liu, Runsheng Chen, X Shirley Liu
Genome Biol. 2007; 8(8): R178. Published online 2007 August 29. doi: 10.1186/gb-2007-8-8-r178
PMCID:
PMC2375008
Abstract Full Text PDF–1.0M
Normalization and experimental design for ChIP-chip data
Shouyong Peng, Artyom A Alekseyenko, Erica Larschan, Mitzi I Kuroda, Peter J Park
BMC Bioinformatics. 2007; 8: 219. Published online 2007 June 25. doi: 10.1186/1471-2105-8-219
PMCID:
PMC1913544
Abstract Full Text PDF–1.3M
Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips
Andrew P Harrison, Caroline E Johnston, Christine A Orengo
BMC Bioinformatics. 2007; 8: 195. Published online 2007 June 11. doi: 10.1186/1471-2105-8-195
PMCID:
PMC1904248
Abstract Full Text PDF–848K
Towards the uniform distribution of null P values on Affymetrix microarrays
Anthony A Fodor, Timothy L Tickle, Christine Richardson
Genome Biol. 2007; 8(5): R69. Published online 2007 May 1. doi: 10.1186/gb-2007-8-5-r69
PMCID:
PMC1929139
Abstract Full Text PDF–6.8M Supplementary Material
ProCAT: a data analysis approach for protein microarrays
Xiaowei Zhu, Mark Gerstein, Michael Snyder
Genome Biol. 2006; 7(11): R110. Published online 2006 November 16. doi: 10.1186/gb-2006-7-11-r110
PMCID:
PMC1794587
Abstract Full Text PDF–830K Supplementary Material
The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies
Roel GW Verhaak, Frank JT Staal, Peter JM Valk, Bob Lowenberg, Marcel JT Reinders, Dick de Ridder
BMC Bioinformatics. 2006; 7: 105. Published online 2006 March 2. doi: 10.1186/1471-2105-7-105
PMCID:
PMC1481623
Abstract Full Text PDF–1.0M Supplementary Material
Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data
Kerby Shedden, Wei Chen, Rork Kuick, Debashis Ghosh, James Macdonald, Kathleen R Cho, Thomas J Giordano, Stephen B Gruber, Eric R Fearon, Jeremy MG Taylor, Samir Hanash
BMC Bioinformatics. 2005; 6: 26. Published online 2005 February 10. doi: 10.1186/1471-2105-6-26
PMCID:
PMC550659
Abstract Full Text PDF–420K
Classification between normal and tumor tissues based on the pair-wise gene expression ratio
YeeLeng Yap, XueWu Zhang, MT Ling, XiangHong Wang, YC Wong, Antoine Danchin
BMC Cancer. 2004; 4: 72. Published online 2004 October 7. doi: 10.1186/1471-2407-4-72
PMCID:
PMC524507
Abstract Full Text PDF–463K
Model selection and efficiency testing for normalization of cDNA microarray data
Matthias Futschik, Toni Crompton
Genome Biol. 2004; 5(8): R60. Published online 2004 July 30. doi: 10.1186/gb-2004-5-8-r60
PMCID:
PMC507885
Abstract Full Text PDF–2.4M Supplementary Material
Improving the scaling normalization for high-density oligonucleotide GeneChip expression microarrays
Chao Lu
BMC Bioinformatics. 2004; 5: 103. Published online 2004 July 29. doi: 10.1186/1471-2105-5-103
PMCID:
PMC509236
Abstract Full Text PDF–363K
Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays
Leah Barrera, Chris Benner, Yong-Chuan Tao, Elizabeth Winzeler, Yingyao Zhou
BMC Bioinformatics. 2004; 5: 42. Published online 2004 April 20. doi: 10.1186/1471-2105-5-42
PMCID:
PMC411067
Abstract Full Text PDF–1.7M
ExpressYourself: a modular platform for processing and visualizing microarray data
Nicholas M. Luscombe, Thomas E. Royce, Paul Bertone, Nathaniel Echols, Christine E. Horak, Joseph T. Chang, Michael Snyder, Mark Gerstein
Nucleic Acids Res. 2003 July 1; 31(13): 3477–3482.
PMCID:
PMC169034
Abstract Full Text PDF–471K
Modeling of DNA microarray data by using physical properties of hybridization
G. A. Held, G. Grinstein, Y. Tu
Proc Natl Acad Sci U S A. 2003 June 24; 100(13): 7575–7580. Published online 2003 June 13. doi: 10.1073/pnas.0832500100
PMCID:
PMC164628
Abstract Full Text PDF–362K Supplementary Material
Long mRNAs coding for yeast mitochondrial proteins of prokaryotic origin preferentially localize to the vicinity of mitochondria
Julien Sylvestre, Stéphane Vialette, Marisol Corral Debrinski, Claude Jacq
Genome Biol. 2003; 4(7): R44. Published online 2003 June 6. doi: 10.1186/gb-2003-4-7-r44
PMCID:
PMC193631
Abstract Full Text PDF–219K Supplementary Material
Improved analytical methods for microarray-based genome-composition analysis
Charles C Kim, Elizabeth A Joyce, Kaman Chan, Stanley Falkow
Genome Biol. 2002; 3(11): research0065.1–research0065.17. Published online 2002 October 29.
PMCID:
PMC133449
Abstract Full Text PDF–506K Supplementary Material
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