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Feature-level exploration of a published Affymetrix GeneChip control dataset
Rafael A Irizarry, Leslie M Cope, Zhijin Wu
Genome Biol. 2006; 7(8): 404. Published online 2006 September 1. doi: 10.1186/gb-2006-7-8-404
PMCID:
PMC1779590
Abstract Full Text PDF–381K Supplementary Material
 Is Cited by the Following 20 Articles in this Archive:
Kernel density weighted loess normalization improves the performance of detection within asymmetrical data
Wen-Ping Hsieh, Tzu-Ming Chu, Yu-Min Lin, Russell D Wolfinger
BMC Bioinformatics. 2011; 12: 222. Published online 2011 June 1. doi: 10.1186/1471-2105-12-222
PMCID:
PMC3118355
Abstract Full Text PDF–479K Supplementary Material
The impact of quantitative optimization of hybridization conditions on gene expression analysis
Peter Sykacek, David P Kreil, Lisa A Meadows, Richard P Auburn, Bettina Fischer, Steven Russell, Gos Micklem
BMC Bioinformatics. 2011; 12: 73. Published online 2011 March 14. doi: 10.1186/1471-2105-12-73
PMCID:
PMC3065421
Abstract Full Text PDF–544K
LTR: Linear Cross-Platform Integration of Microarray Data
Paul C. Boutros
Cancer Inform. 2010; 9: 197–208. Published online 2010 August 27.
PMCID:
PMC2935818
Abstract Full Text PDF–4.5M
A framework for oligonucleotide microarray preprocessing
Benilton S. Carvalho, Rafael A. Irizarry
Bioinformatics. 2010 October 1; 26(19): 2363–2367. Published online 2010 August 5. doi: 10.1093/bioinformatics/btq431
PMCID:
PMC2944196
Abstract Full Text PDF–493K Supplementary Material
Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset
Qianqian Zhu, Jeffrey C Miecznikowski, Marc S Halfon
BMC Bioinformatics. 2010; 11: 285. Published online 2010 May 27. doi: 10.1186/1471-2105-11-285
PMCID:
PMC2897828
Abstract Full Text PDF–5.1M Supplementary Material
Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset
Qianqian Zhu, Jeffrey C Miecznikowski, Marc S Halfon
BMC Bioinformatics. 2010; 11: 285. Published online 2010 May 27. doi: 10.1186/1471-2105-11-285
PMCID:
PMC2897828
Abstract Full Text PDF–5.1M Supplementary Material
A comparison of probe-level and probeset models for small-sample gene expression data
John R Stevens, Jason L Bell, Kenneth I Aston, Kenneth L White
BMC Bioinformatics. 2010; 11: 281. Published online 2010 May 26. doi: 10.1186/1471-2105-11-281
PMCID:
PMC2901368
Abstract Full Text PDF–4.2M
Supervised normalization of microarrays
Brigham H. Mecham, Peter S. Nelson, John D. Storey
Bioinformatics. 2010 May 15; 26(10): 1308–1315. Published online 2010 March 31. doi: 10.1093/bioinformatics/btq118
PMCID:
PMC2865860
Abstract Full Text PDF–384K Supplementary Material
Performance evaluation of commercial miRNA expression array platforms
Sachin Sah, Matthew N McCall, Deepa Eveleigh, Michael Wilson, Rafael A Irizarry
BMC Res Notes. 2010; 3: 80. Published online 2010 March 18. doi: 10.1186/1756-0500-3-80
PMCID:
PMC2853548
Abstract Full Text PDF–873K Supplementary Material
A benchmark for statistical microarray data analysis that preserves actual biological and technical variance
Benoît De Hertogh, Bertrand De Meulder, Fabrice Berger, Michael Pierre, Eric Bareke, Anthoula Gaigneaux, Eric Depiereux
BMC Bioinformatics. 2010; 11: 17. Published online 2010 January 11. doi: 10.1186/1471-2105-11-17
PMCID:
PMC2831002
Abstract Full Text PDF–741K Supplementary Material
A close examination of double filtering with fold change and t test in microarray analysis
Song Zhang, Jing Cao
BMC Bioinformatics. 2009; 10: 402. Published online 2009 December 8. doi: 10.1186/1471-2105-10-402
PMCID:
PMC2801685
Abstract Full Text PDF–373K
A first principles approach to differential expression in microarray data analysis
Robert A Rubin
BMC Bioinformatics. 2009; 10: 292. Published online 2009 September 16. doi: 10.1186/1471-2105-10-292
PMCID:
PMC2749840
Abstract Full Text PDF–745K
Bayesian optimal discovery procedure for simultaneous significance testing
Jing Cao, Xian-Jin Xie, Song Zhang, Angelique Whitehurst, Michael A White
BMC Bioinformatics. 2009; 10: 5. Published online 2009 January 6. doi: 10.1186/1471-2105-10-5
PMCID:
PMC2628883
Abstract Full Text PDF–347K Supplementary Material
Use of normalization methods for analysis of microarrays containing a high degree of gene effects
Terri T Ni, William J Lemon, Yu Shyr, Tao P Zhong
BMC Bioinformatics. 2008; 9: 505. Published online 2008 November 28. doi: 10.1186/1471-2105-9-505
PMCID:
PMC2612699
Abstract Full Text PDF–469K Supplementary Material
Background correction using dinucleotide affinities improves the performance of GCRMA
Raad Z Gharaibeh, Anthony A Fodor, Cynthia J Gibas
BMC Bioinformatics. 2008; 9: 452. Published online 2008 October 23. doi: 10.1186/1471-2105-9-452
PMCID:
PMC2579310
Abstract Full Text PDF–454K Supplementary Material
Effects of Aneuploidy on Genome Structure, Expression, and Interphase Organization in Arabidopsis thaliana
Bruno Huettel, David P. Kreil, Marjori Matzke, Antonius J. M. Matzke
PLoS Genet. 2008 October; 4(10): e1000226. Published online 2008 October 17. doi: 10.1371/journal.pgen.1000226
PMCID:
PMC2562519
Abstract Full Text PDF–479K Supplementary Material
Consolidated strategy for the analysis of microarray spike-in data
Matthew N. McCall, Rafael A. Irizarry
Nucleic Acids Res. 2008 October; 36(17): e108. Published online 2008 October. doi: 10.1093/nar/gkn430
PMCID:
PMC2553586
Abstract Full Text PDF–236K Supplementary Material
"Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures
Hans Binder, Knut Krohn, Stephan Preibisch
Algorithms Mol Biol. 2008; 3: 11. Published online 2008 August 29. doi: 10.1186/1748-7188-3-11
PMCID:
PMC2543012
Abstract Full Text PDF–3.9M
A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods
Richard D Pearson
BMC Bioinformatics. 2008; 9: 164. Published online 2008 March 26. doi: 10.1186/1471-2105-9-164
PMCID:
PMC2324099
Abstract Full Text PDF–473K Supplementary Material
Fisher's combined p-value for detecting differentially expressed genes using Affymetrix expression arrays
Ann Hess, Hari Iyer
BMC Genomics. 2007; 8: 96. Published online 2007 April 9. doi: 10.1186/1471-2164-8-96
PMCID:
PMC1854896
Abstract Full Text PDF–614K
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