Genome Biology

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A reanalysis of a published Affymetrix GeneChip control dataset

Alan R Dabney and John D Storey*

Genome Biology 2006, 7:401 doi:10.1186/gb-2006-7-3-401

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Methodology article   Open Access

A benchmark for statistical microarray data analysis that preserves actual biological and technical variance

BenoƮt De Hertogh, Bertrand De Meulder, Fabrice Berger, Michael Pierre, Eric Bareke, Anthoula Gaigneaux, Eric Depiereux BMC Bioinformatics 2010, 11:17 (11 January 2010)

Research   Open Access

A distribution-free convolution model for background correction of oligonucleotide microarray data

Zhongxue Chen, Monnie McGee, Qingzhong Liu, Megan Kong, Youping Deng, Richard H Scheuermann BMC Genomics 2009, 10(Suppl 1):S19 (7 July 2009)

Methodology article   Open Access

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 (6 January 2009)

Methodology article   Open Access

Background correction using dinucleotide affinities improves the performance of GCRMA

Raad Z Gharaibeh, Anthony A Fodor, Cynthia J Gibas BMC Bioinformatics 2008, 9:452 (23 October 2008)

Research article   Open Access

A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods

Richard D Pearson BMC Bioinformatics 2008, 9:164 (26 March 2008)

Research article   Open Access Highly Accessed

The utility of MAS5 expression summary and detection call algorithms

Stuart D Pepper, Emma K Saunders, Laura E Edwards, Claire L Wilson, Crispin J Miller BMC Bioinformatics 2007, 8:273 (30 July 2007)

Research article   Open Access Highly Accessed

Pre-processing Agilent microarray data

Marianna Zahurak, Giovanni Parmigiani, Wayne Yu, Robert B Scharpf, David Berman, Edward Schaeffer, Shabana Shabbeer, Leslie Cope BMC Bioinformatics 2007, 8:142 (1 May 2007)

Method   Open Access

Towards the uniform distribution of null P values on Affymetrix microarrays

Anthony A Fodor, Timothy L Tickle, Christine Richardson Genome Biology 2007, 8:R69 (1 May 2007)

Estimating the P value from the overall distribution of scores on the microarray can produce P values that are much closer to a uniform distribution.

Research article   Open Access

Putative null distributions corresponding to tests of differential expression in the Golden Spike dataset are intensity dependent

Daniel P Gaile, Jeffrey C Miecznikowski BMC Genomics 2007, 8:105 (19 April 2007)

Methodology article   Open Access Highly Accessed

Fisher's combined p-value for detecting differentially expressed genes using Affymetrix expression arrays

Ann Hess, Hari Iyer BMC Genomics 2007, 8:96 (9 April 2007)

Method   Open Access Highly Accessed

Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships

Alan R Dabney, John D Storey Genome Biology 2007, 8:R44 (28 March 2007)

eCADS is a new method for multiple array normalization of two-channel microarrays that takes into account general experimental designs and intensity-dependent relationships and allows for a more efficient dye-swap design that requires only one array per sample pair.

Research article   Open Access Highly Accessed

Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments

Maureen A Sartor, Craig R Tomlinson, Scott C Wesselkamper, Siva Sivaganesan, George D Leikauf, Mario Medvedovic BMC Bioinformatics 2006, 7:538 (19 December 2006)

Methodology   Open Access

The Shivplot: a graphical display for trend elucidation and exploratory analysis of microarray data

Owen Z Woody, Robert Nadon Source Code for Biology and Medicine 2006, 1:6 (8 November 2006)

Correspondence   Free

Feature-level exploration of a published Affymetrix GeneChip control dataset

Rafael A Irizarry, Leslie M Cope, Zhijin Wu Genome Biology 2006, 7:404 (1 September 2006)

A comment on Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset by SE Choe, M Boutros, AM Michelson, GM Church and MS Halfon. Genome Biology 2005, 6:R16