Genome Biology

official impact factor 6.89

Open Access Highly Access

Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset

Sung E Choe, Michael Boutros, Alan M Michelson, George M Church and Marc S Halfon*

Genome Biology 2005, 6:R16 doi:10.1186/gb-2005-6-2-r16

Accesses  

  • Last 30 days: 108 accesses
  • Last year: 1546 accesses
  • All time: 23127 accesses

Cited by

BioMed Central: 57 citations

Research article   Open Access

Exploring the use of internal and externalcontrols for assessing microarray technical performance

Katrice A Lippa, David L Duewer, Marc L Salit, Laurence Game, Helen C Causton BMC Research Notes 2010, 3:349 (28 December 2010)

This article is part of a collection on Microarray normalization...

Methodology article   Open Access

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 (11 January 2010)

Research article   Open Access Highly Accessed

A close examination of double filtering with fold change and t test in microarray analysis

Song Zhang, Jing Cao BMC Bioinformatics 2009, 10:402 (8 December 2009)

Double filtering using fold change and t test to find differentially expressed genes loses power due to differing assumptions about variance, whereas combining Bayesian mixture models with SAM approaches the performance of the theoretically best likelihood ratio test statistic.

Research   Open Access Highly Accessed

Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers

Jonathan M Dreyfuss, Mark D Johnson, Peter J Park Molecular Cancer 2009, 8:71 (4 September 2009)

Methodology article   Open Access Highly Accessed

Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene Ontology

Tao Xu, JianLei Gu, Yan Zhou, LinFang Du BMC Bioinformatics 2009, 10:240 (5 August 2009)

Research article   Open Access

Gene expression profile of rat left ventricles reveals persisting changes following chronic mild exercise protocol: implications for cardioprotection

Betti Giusti, Marina Marini, Luciana Rossi, Ilaria Lapini, Alberto Magi, Andrea Capalbo, Rosa Lapalombella, Simona di Tullio, Michele Samaja, Fabio Esposito, Vittoria Margonato, Maria Boddi, Rosanna Abbate, Arsenio Veicsteinas BMC Genomics 2009, 10:342 (30 July 2009)

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)

Research   Open Access Highly Accessed

Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity

Koji Kadota, Yuji Nakai, Kentaro Shimizu Algorithms for Molecular Biology 2009, 4:7 (22 April 2009)

Methodology article   Open Access Highly Accessed

Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees

Donna M Toleno, Gabriel Renaud, Tyra G Wolfsberg, Munirul Islam, Derek E Wildman, Kimberly D Siegmund, Joseph G Hacia BMC Bioinformatics 2009, 10:77 (5 March 2009)

Research   Open Access

Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations

Reija Autio, Sami Kilpinen, Matti Saarela, Olli Kallioniemi, Sampsa Hautaniemi, Jaakko Astola BMC Bioinformatics 2009, 10(Suppl 1):S24 (30 January 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

Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data

Carl R Pelz, Molly Kulesz-Martin, Grover Bagby, Rosalie C Sears BMC Bioinformatics 2008, 9:520 (4 December 2008)

Methodology article   Open Access

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 (28 November 2008)

Research article   Open Access

Dissecting an alternative splicing analysis workflow for GeneChip® Exon 1.0 ST Affymetrix arrays

Cristina Della Beffa, Francesca Cordero, Raffaele A Calogero BMC Genomics 2008, 9:571 (28 November 2008)

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)

Method   Open Access Highly Accessed

Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues

Sami Kilpinen, Reija Autio, Kalle Ojala, Kristiina Iljin, Elmar Bucher, Henri Sara, Tommi Pisto, Matti Saarela, Rolf I Skotheim, Mari Björkman, John-Patrick Mpindi, Saija Haapa-Paananen, Paula Vainio, Henrik Edgren, Maija Wolf, Jaakko Astola, Matthias Nees, Sampsa Hautaniemi, Olli Kallioniemi Genome Biology 2008, 9:R139 (19 September 2008)

A method for the comparison of mRNA expression levels of most human genes across gene expression array experiments, and a database of the results, are presented.

Research   Open Access Highly Accessed

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

Hans Binder, Knut Krohn, Stephan Preibisch Algorithms for Molecular Biology 2008, 3:11 (29 August 2008)

Methodology article   Open Access

A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays

Huanying Ge, Chao Cheng, Lei M Li BMC Bioinformatics 2008, 9:194 (14 April 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)

Methodology article   Open Access Highly Accessed

Empirical Bayes models for multiple probe type microarrays at the probe level

Magnus Åstrand, Petter Mostad, Mats Rudemo BMC Bioinformatics 2008, 9:156 (20 March 2008)

Research article   Open Access Highly Accessed

Normalization of oligonucleotide arrays based on the least-variant set of genes

Stefano Calza, Davide Valentini, Yudi Pawitan BMC Bioinformatics 2008, 9:140 (5 March 2008)

Research article   Open Access

Effect of thyroid hormone concentration on the transcriptional response underlying induced metamorphosis in the Mexican axolotl (Ambystoma)

Robert B Page, Stephen R Voss, Amy K Samuels, Jeramiah J Smith, Srikrishna Putta, Christopher K Beachy BMC Genomics 2008, 9:78 (11 February 2008)

Method   Open Access Highly Accessed

Correction of technical bias in clinical microarray data improves concordance with known biological information

Aron C Eklund, Zoltan Szallasi Genome Biology 2008, 9:R26 (4 February 2008)

A method is presented to correct for technical bias in clinical microarray data, which increases concordance with known biological relationships.

Software   Open Access

BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips

Ernest Turro, Natalia Bochkina, Anne-Mette K Hein, Sylvia Richardson BMC Bioinformatics 2007, 8:439 (12 November 2007)

Research article   Open Access Highly Accessed

Vascular microarray profiling in two models of hypertension identifies caveolin-1, Rgs2 and Rgs5 as antihypertensive targets

T Hilton Grayson, Stephen J Ohms, Therese D Brackenbury, Kate R Meaney, Kaiman Peng, Yvonne E Pittelkow, Susan R Wilson, Shaun L Sandow, Caryl E Hill BMC Genomics 2007, 8:404 (7 November 2007)

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)

Methodology article   Open Access

Post hoc pattern matching: assigning significance to statistically defined expression patterns in single channel microarray data

Randall Hulshizer, Eric M Blalock BMC Bioinformatics 2007, 8:240 (5 July 2007)

Research   Open Access

Evolutionary conservation of regulated longevity assurance mechanisms

Joshua J McElwee, Eugene Schuster, Eric Blanc, Matthew D Piper, James H Thomas, Dhaval S Patel, Colin Selman, Dominic J Withers, Janet M Thornton, Linda Partridge, David Gems Genome Biology 2007, 8:R132 (5 July 2007)

Short abstract: A multi-level cross-species comparative analysis of gene-expression changes accompanying increased longevity in mutant nematodes, fruit flies and mice with reduced insulin/IGF-1 signaling revealed candidate conserved mechanisms.

Method   Open Access

Correcting for sequence biases in present/absent calls

Eugene F Schuster, Eric Blanc, Linda Partridge, Janet M Thornton Genome Biology 2007, 8:R125 (26 June 2007)

Correction of non-specific binding for both PM and MM probes using probe-sequence models can partially remove the probe-sequence bias in Affymetrix microarray experiments and result in better performance of the MAS 5.0 algorithm.

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)

Methodology article   Open Access

Gene selection with multiple ordering criteria

James J Chen, Chen-An Tsai, ShengLi Tzeng, Chun-Houh Chen BMC Bioinformatics 2007, 8:74 (5 March 2007)

Research article   Open Access

Detecting differential expression in microarray data: comparison of optimal procedures

Elena Perelman, Alexander Ploner, Stefano Calza, Yudi Pawitan BMC Bioinformatics 2007, 8:28 (26 January 2007)

Research   Open Access

Impairment of organ-specific T cell negative selection by diabetes susceptibility genes: genomic analysis by mRNA profiling

Adrian Liston, Kristine Hardy, Yvonne Pittelkow, Susan R Wilson, Lydia E Makaroff, Aude M Fahrer, Christopher C Goodnow Genome Biology 2007, 8:R12 (21 January 2007)

A transcription profiling study, together with genetic linkage data, provides a molecular map of the T-cell negative selection response in vivo.

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)

Research article   Open Access

Analyzing the dose-dependence of the Saccharomyces cerevisiae global transcriptional response to methyl methanesulfonate and ionizing radiation

Michael G Benton, Swetha Somasundaram, Jeremy D Glasner, Sean P Palecek BMC Genomics 2006, 7:305 (1 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)

Methodology article   Open Access

A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database

Simon Katz, Rafael A Irizarry, Xue Lin, Mark Tripputi, Mark W Porter BMC Bioinformatics 2006, 7:464 (23 October 2006)

Research   Open Access

Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution

Jaroslav P Novak, Seon-Young Kim, Jun Xu, Olga Modlich, David J Volsky, David Honys, Joan L Slonczewski, Douglas A Bell, Fred R Blattner, Eduardo Blumwald, Marjan Boerma, Manuel Cosio, Zoran Gatalica, Marian Hajduch, Juan Hidalgo, Roderick R McInnes, Merrill C Miller III, Milena Penkowa, Michael S Rolph, Jordan Sottosanto, Rene St-Arnaud, Michael J Szego, David Twell, Charles Wang Biology Direct 2006, 1:27 (7 September 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

Research article   Open Access

Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression

Sébastien Lemieux BMC Bioinformatics 2006, 7:391 (25 August 2006)

Methodology article   Open Access

Robust computational reconstitution – a new method for the comparative analysis of gene expression in tissues and isolated cell fractions

Martin Hoffmann, Dirk Pohlers, Dirk Koczan, Hans-Jürgen Thiesen, Stefan Wölfl, Raimund W Kinne BMC Bioinformatics 2006, 7:369 (4 August 2006)

Research article   Open Access Highly Accessed

Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data

Ian B Jeffery, Desmond G Higgins, Aedín C Culhane BMC Bioinformatics 2006, 7:359 (26 July 2006)

Research article   Open Access Highly Accessed

A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates

Anne-Mette K Hein, Sylvia Richardson BMC Bioinformatics 2006, 7:353 (20 July 2006)

Research   Open Access

Variation in fiberoptic bead-based oligonucleotide microarrays: dispersion characteristics among hybridization and biological replicate samples

Jaroslav P Novak, Merrill C Miller, Douglas A Bell Biology Direct 2006, 1:18 (20 June 2006)

Research article   Open Access Highly Accessed

Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression

LanMin Zhang, Sean J Yoder, Steven A Enkemann BMC Genomics 2006, 7:153 (15 June 2006)

Methodology article   Open Access

Correction of scaling mismatches in oligonucleotide microarray data

Martino Barenco, Jaroslav Stark, Daniel Brewer, Daniela Tomescu, Robin Callard, Michael Hubank BMC Bioinformatics 2006, 7:251 (9 May 2006)

Methodology article   Open Access

A comparison of alternative 60-mer probe designs in an in-situ synthesized oligonucleotide microarray

Danielle L Leiske, Anis Karimpour-Fard, Patrick S Hume, Benjamin D Fairbanks, Ryan T Gill BMC Genomics 2006, 7:72 (4 April 2006)

Correspondence   Free Highly Accessed

A reanalysis of a published Affymetrix GeneChip control dataset

Alan R Dabney, John D Storey Genome Biology 2006, 7:401 (22 March 2006)

A response to 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

Research article   Open Access Highly Accessed

How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results

Frank F Millenaar, John Okyere, Sean T May, Martijn van Zanten, Laurentius ACJ Voesenek, Anton JM Peeters BMC Bioinformatics 2006, 7:137 (15 March 2006)

Research article   Open Access Highly Accessed

Evaluation of methods for oligonucleotide array data via quantitative real-time PCR

Li-Xuan Qin, Richard P Beyer, Francesca N Hudson, Nancy J Linford, Daryl E Morris, Kathleen F Kerr BMC Bioinformatics 2006, 7:23 (17 January 2006)

Methodology article   Open Access Highly Accessed

Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies

Zihua Hu, Gail R Willsky BMC Bioinformatics 2006, 7:12 (10 January 2006)

Methodology article   Open Access Highly Accessed

Proposed methods for testing and selecting the ERCC external RNA controls

BMC Genomics 2005, 6:150 (2 November 2005)

Methodology article   Open Access

Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach

Jun Lu, John K Tomfohr, Thomas B Kepler BMC Bioinformatics 2005, 6:165 (29 June 2005)

Methodology article   Open Access

Correlation test to assess low-level processing of high-density oligonucleotide microarray data

Alexander Ploner, Lance D Miller, Per Hall, Jonas Bergh, Yudi Pawitan BMC Bioinformatics 2005, 6:80 (31 March 2005)

A new graphical method for assessing the quality of low-level analysis of microarray expression data shows, among other things, that normalization, while necessary, should not be based on housekeeping genes.