Skip Navigation


Bioinformatics Advance Access originally published online on January 18, 2005
Bioinformatics 2005 21(9):2067-2075; doi:10.1093/bioinformatics/bti270
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/9/2067    most recent
bti270v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (103)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Smyth, G. K.
Right arrow Articles by Scott, H. S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Smyth, G. K.
Right arrow Articles by Scott, H. S.
Social Bookmarking
 Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Use of within-array replicate spots for assessing differential expression in microarray experiments

Gordon K. Smyth *, Joëlle Michaud and Hamish S. Scott

Walter and Eliza Hall Institute of Medical Research Melbourne, Vic 3050, Australia

*To whom correspondence should be addressed.

Motivation: Spotted arrays are often printed with probes in duplicate or triplicate, but current methods for assessing differential expression are not able to make full use of the resulting information. The usual practice is to average the duplicate or triplicate results for each probe before assessing differential expression. This results in the loss of valuable information about genewise variability.

Results: A method is proposed for extracting more information from within-array replicate spots in microarray experiments by estimating the strength of the correlation between them. The method involves fitting separate linear models to the expression data for each gene but with a common value for the between-replicate correlation. The method greatly improves the precision with which the genewise variances are estimated and thereby improves inference methods designed to identify differentially expressed genes. The method may be combined with empirical Bayes methods for moderating the genewise variances between genes. The method is validated using data from a microarray experiment involving calibration and ratio control spots in conjunction with spiked-in RNA. Comparing results for calibration and ratio control spots shows that the common correlation method results in substantially better discrimination of differentially expressed genes from those which are not. The spike-in experiment also confirms that the results may be further improved by empirical Bayes smoothing of the variances when the sample size is small.

Availability: The methodology is implemented in the limma software package for R, available from the CRAN repository http://www.r-project.org

Contact: smyth{at}wehi.edu.au


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
J. Biol. Chem.Home page
B. Schade, T. Rao, N. Dourdin, R. Lesurf, M. Hallett, R. D. Cardiff, and W. J. Muller
PTEN Deficiency in a Luminal ErbB-2 Mouse Model Results in Dramatic Acceleration of Mammary Tumorigenesis and Metastasis
J. Biol. Chem., July 10, 2009; 284(28): 19018 - 19026.
[Abstract] [Full Text] [PDF]


Home page
Mol PlantHome page
L. Song, X.-Y. Zhou, L. Li, L.-J. Xue, X. Yang, and H.-W. Xue
Genome-Wide Analysis Revealed the Complex Regulatory Network of Brassinosteroid Effects in Photomorphogenesis
Mol Plant, June 23, 2009; (2009) ssp039v1.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
Y. Benita, H. Kikuchi, A. D. Smith, M. Q. Zhang, D. C. Chung, and R. J. Xavier
An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia
Nucleic Acids Res., June 2, 2009; (2009) gkp425v1.
[Abstract] [Full Text] [PDF]


Home page
Plant Physiol.Home page
B. Singh, U. Avci, S. E. Eichler Inwood, M. J. Grimson, J. Landgraf, D. Mohnen, I. Sorensen, C. G. Wilkerson, W. G.T. Willats, and C. H. Haigler
A Specialized Outer Layer of the Primary Cell Wall Joins Elongating Cotton Fibers into Tissue-Like Bundles
Plant Physiology, June 1, 2009; 150(2): 684 - 699.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
H. Guo, L. Li, H. Ye, X. Yu, A. Algreen, and Y. Yin
Three related receptor-like kinases are required for optimal cell elongation in Arabidopsis thaliana
PNAS, May 5, 2009; 106(18): 7648 - 7653.
[Abstract] [Full Text] [PDF]


Home page
Cancer Res.Home page
V. C. Daniel, L. Marchionni, J. S. Hierman, J. T. Rhodes, W. L. Devereux, C. M. Rudin, R. Yung, G. Parmigiani, M. Dorsch, C. D. Peacock, et al.
A Primary Xenograft Model of Small-Cell Lung Cancer Reveals Irreversible Changes in Gene Expression Imposed by Culture In vitro
Cancer Res., April 15, 2009; 69(8): 3364 - 3373.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
P. Leprohon, D. Legare, F. Raymond, E. Madore, G. Hardiman, J. Corbeil, and M. Ouellette
Gene expression modulation is associated with gene amplification, supernumerary chromosomes and chromosome loss in antimony-resistant Leishmania infantum
Nucleic Acids Res., April 1, 2009; 37(5): 1387 - 1399.
[Abstract] [Full Text] [PDF]


Home page
J. Immunol.Home page
R. Brambilla, T. Persaud, X. Hu, S. Karmally, V. I. Shestopalov, G. Dvoriantchikova, D. Ivanov, L. Nathanson, S. R. Barnum, and J. R. Bethea
Transgenic Inhibition of Astroglial NF-{kappa}B Improves Functional Outcome in Experimental Autoimmune Encephalomyelitis by Suppressing Chronic Central Nervous System Inflammation
J. Immunol., March 1, 2009; 182(5): 2628 - 2640.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
S. G. Dashper, C.-S. Ang, P. D. Veith, H. L. Mitchell, A. W. H. Lo, C. A. Seers, K. A. Walsh, N. Slakeski, D. Chen, J. P. Lissel, et al.
Response of Porphyromonas gingivalis to Heme Limitation in Continuous Culture
J. Bacteriol., February 1, 2009; 191(3): 1044 - 1055.
[Abstract] [Full Text] [PDF]


Home page
Genome ResHome page
L. Milani, A. Lundmark, J. Nordlund, A. Kiialainen, T. Flaegstad, G. Jonmundsson, J. Kanerva, K. Schmiegelow, K. L. Gunderson, G. Lonnerholm, et al.
Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation
Genome Res., January 1, 2009; 19(1): 1 - 11.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
F. Hommais, C. Oger-Desfeux, F. Van Gijsegem, S. Castang, S. Ligori, D. Expert, W. Nasser, and S. Reverchon
PecS Is a Global Regulator of the Symptomatic Phase in the Phytopathogenic Bacterium Erwinia chrysanthemi 3937
J. Bacteriol., November 15, 2008; 190(22): 7508 - 7522.
[Abstract] [Full Text] [PDF]


Home page
Appl. Environ. Microbiol.Home page
K. Lemuth, T. Hardiman, S. Winter, D. Pfeiffer, M. A. Keller, S. Lange, M. Reuss, R. D. Schmid, and M. Siemann-Herzberg
Global Transcription and Metabolic Flux Analysis of Escherichia coli in Glucose-Limited Fed-Batch Cultivations
Appl. Envir. Microbiol., November 15, 2008; 74(22): 7002 - 7015.
[Abstract] [Full Text] [PDF]


Home page
Eukaryot CellHome page
M. M. Abhyankar, A. E. Hochreiter, J. Hershey, C. Evans, Y. Zhang, O. Crasta, B. W. S. Sobral, B. J. Mann, W. A. Petri Jr., and C. A. Gilchrist
Characterization of an Entamoeba histolytica High-Mobility-Group Box Protein Induced during Intestinal Infection
Eukaryot. Cell, September 1, 2008; 7(9): 1565 - 1572.
[Abstract] [Full Text] [PDF]


Home page
EndocrinologyHome page
D. Diez, C. Grijota-Martinez, P. Agretti, G. De Marco, M. Tonacchera, A. Pinchera, G. Morreale de Escobar, J. Bernal, and B. Morte
Thyroid Hormone Action in the Adult Brain: Gene Expression Profiling of the Effects of Single and Multiple Doses of Triiodo-L-Thyronine in the Rat Striatum
Endocrinology, August 1, 2008; 149(8): 3989 - 4000.
[Abstract] [Full Text] [PDF]


Home page
CarcinogenesisHome page
E. Hervouet, A. Cizkova, J. Demont, A. Vojtiskova, P. Pecina, N. L.W. Franssen-van Hal, J. Keijer, H. Simonnet, R. Ivanek, S. Kmoch, et al.
HIF and reactive oxygen species regulate oxidative phosphorylation in cancer
Carcinogenesis, August 1, 2008; 29(8): 1528 - 1537.
[Abstract] [Full Text] [PDF]


Home page
J. Am. Soc. Nephrol.Home page
M. J. Vitalone, P. J. O'Connell, E. Jimenez-Vera, A. Yuksel, M. Wavamunno, C. L.-S. Fung, J. R. Chapman, and B. J. Nankivell
Epithelial-to-Mesenchymal Transition in Early Transplant Tubulointerstitial Damage
J. Am. Soc. Nephrol., August 1, 2008; 19(8): 1571 - 1583.
[Abstract] [Full Text] [PDF]


Home page
Plant CellHome page
C.-y. Wu, A. Trieu, P. Radhakrishnan, S. F. Kwok, S. Harris, K. Zhang, J. Wang, J. Wan, H. Zhai, S. Takatsuto, et al.
Brassinosteroids Regulate Grain Filling in Rice
PLANT CELL, August 1, 2008; 20(8): 2130 - 2145.
[Abstract] [Full Text] [PDF]


Home page
Genes Dev.Home page
Y. Ghavi-Helm, M. Michaut, J. Acker, J.-C. Aude, P. Thuriaux, M. Werner, and J. Soutourina
Genome-wide location analysis reveals a role of TFIIS in RNA polymerase III transcription
Genes & Dev., July 15, 2008; 22(14): 1934 - 1947.
[Abstract] [Full Text] [PDF]


Home page
Plant Physiol.Home page
D. Riewe, L. Grosman, A. R. Fernie, C. Wucke, and P. Geigenberger
The Potato-Specific Apyrase Is Apoplastically Localized and Has Influence on Gene Expression, Growth, and Development
Plant Physiology, July 1, 2008; 147(3): 1092 - 1109.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
A. Y.-L. So, S. B. Cooper, B. J. Feldman, M. Manuchehri, and K. R. Yamamoto
Conservation analysis predicts in vivo occupancy of glucocorticoid receptor-binding sequences at glucocorticoid-induced genes
PNAS, April 15, 2008; 105(15): 5745 - 5749.
[Abstract] [Full Text] [PDF]


Home page
Clin. Chem.Home page
S. Szameit, K. Vierlinger, L. Farmer, H. Tuschl, and C. Noehammer
Microarray-Based In Vitro Test System for the Discrimination of Contact Allergens and Irritants: Identification of Potential Marker Genes
Clin. Chem., March 1, 2008; 54(3): 525 - 533.
[Abstract] [Full Text] [PDF]


Home page
Genome ResHome page
T. Mourier, C. Carret, S. Kyes, Z. Christodoulou, P. P. Gardner, D. C. Jeffares, R. Pinches, B. Barrell, M. Berriman, S. Griffiths-Jones, et al.
Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum
Genome Res., February 1, 2008; 18(2): 281 - 292.
[Abstract] [Full Text] [PDF]


Home page
J. Immunol.Home page
C. Pridans, M. L. Holmes, M. Polli, J. M. Wettenhall, A. Dakic, L. M. Corcoran, G. K. Smyth, and S. L. Nutt
Identification of Pax5 Target Genes in Early B Cell Differentiation
J. Immunol., February 1, 2008; 180(3): 1719 - 1728.
[Abstract] [Full Text] [PDF]


Home page
Appl. Environ. Microbiol.Home page
S. Raengpradub, M. Wiedmann, and K. J. Boor
Comparative Analysis of the {sigma}B-Dependent Stress Responses in Listeria monocytogenes and Listeria innocua Strains Exposed to Selected Stress Conditions
Appl. Envir. Microbiol., January 1, 2008; 74(1): 158 - 171.
[Abstract] [Full Text] [PDF]


Home page
Plant Physiol.Home page
M. Alhagdow, F. Mounet, L. Gilbert, A. Nunes-Nesi, V. Garcia, D. Just, J. Petit, B. Beauvoit, A. R. Fernie, C. Rothan, et al.
Silencing of the Mitochondrial Ascorbate Synthesizing Enzyme L-Galactono-1,4-Lactone Dehydrogenase Affects Plant and Fruit Development in Tomato
Plant Physiology, December 1, 2007; 145(4): 1408 - 1422.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
M. E. Ritchie, J. Silver, A. Oshlack, M. Holmes, D. Diyagama, A. Holloway, and G. K. Smyth
A comparison of background correction methods for two-colour microarrays
Bioinformatics, October 15, 2007; 23(20): 2700 - 2707.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
J. Fan and Y. Niu
Selection and validation of normalization methods for c-DNA microarrays using within-array replications
Bioinformatics, September 15, 2007; 23(18): 2391 - 2398.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
A. Reiner-Benaim, D. Yekutieli, N. E. Letwin, G. I. Elmer, N. H. Lee, N. Kafkafi, and Y. Benjamini
Associating quantitative behavioral traits with gene expression in the brain: searching for diamonds in the hay
Bioinformatics, September 1, 2007; 23(17): 2239 - 2246.
[Abstract] [Full Text] [PDF]


Home page
Biol. Reprod.Home page
Y. Choi, Y. Qin, M. F. Berger, D. J. Ballow, M. L. Bulyk, and A. Rajkovic
Microarray Analyses of Newborn Mouse Ovaries Lacking Nobox
Biol Reprod, August 1, 2007; 77(2): 312 - 319.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
V. J. Armstrong, M. Muzylak, A. Sunters, G. Zaman, L. K. Saxon, J. S. Price, and L. E. Lanyon
Wnt/beta-Catenin Signaling Is a Component of Osteoblastic Bone Cell Early Responses to Load-bearing and Requires Estrogen Receptor {alpha}
J. Biol. Chem., July 13, 2007; 282(28): 20715 - 20727.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
C. Gao, K. Furge, J. Koeman, K. Dykema, Y. Su, M. L. Cutler, A. Werts, P. Haak, and G. F. Vande Woude
Chromosome instability, chromosome transcriptome, and clonal evolution of tumor cell populations
PNAS, May 22, 2007; 104(21): 8995 - 9000.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
A. Oshlack, A. E. Chabot, G. K. Smyth, and Y. Gilad
Using DNA microarrays to study gene expression in closely related species
Bioinformatics, May 15, 2007; 23(10): 1235 - 1242.
[Abstract] [Full Text] [PDF]


Home page
MicrobiologyHome page
M. Shemesh, A. Tam, and D. Steinberg
Differential gene expression profiling of Streptococcus mutans cultured under biofilm and planktonic conditions
Microbiology, May 1, 2007; 153(5): 1307 - 1317.
[Abstract] [Full Text] [PDF]


Home page
J Exp BotHome page
B. Zhou, Y. Li, Z. Xu, H. Yan, S. Homma, and S. Kawabata
Ultraviolet A-specific induction of anthocyanin biosynthesis in the swollen hypocotyls of turnip (Brassica rapa)
J. Exp. Bot., May 1, 2007; 58(7): 1771 - 1781.
[Abstract] [Full Text] [PDF]


Home page
J. Immunol.Home page
M.-P. Puissegur, G. Lay, M. Gilleron, L. Botella, J. Nigou, H. Marrakchi, B. Mari, J.-L. Duteyrat, Y. Guerardel, L. Kremer, et al.
Mycobacterial Lipomannan Induces Granuloma Macrophage Fusion via a TLR2-Dependent, ADAM9- and beta1 Integrin-Mediated Pathway
J. Immunol., March 1, 2007; 178(5): 3161 - 3169.
[Abstract] [Full Text] [PDF]


Home page
Plant CellHome page
J. Lee, K. He, V. Stolc, H. Lee, P. Figueroa, Y. Gao, W. Tongprasit, H. Zhao, I. Lee, and X. W. Deng
Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development
PLANT CELL, March 1, 2007; 19(3): 731 - 749.
[Abstract] [Full Text] [PDF]


Home page
Eukaryot CellHome page
L. Strmecki, G. Bloomfield, T. Araki, E. Dalton, J. Skelton, C. Schilde, A. Harwood, J. G. Williams, A. Ivens, and C. Pears
Proteomic and Microarray Analyses of the Dictyostelium Zak1-GSK-3 Signaling Pathway Reveal a Role in Early Development
Eukaryot. Cell, February 1, 2007; 6(2): 245 - 252.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
D. S. Yuan and R. A. Irizarry
High-resolution spatial normalization for microarrays containing embedded technical replicates
Bioinformatics, December 15, 2006; 22(24): 3054 - 3060.
[Abstract] [Full Text] [PDF]


Home page
Physiol. GenomicsHome page
P. C. LaRosa, J. Miner, Y. Xia, Y. Zhou, S. Kachman, and M. E. Fromm
Trans-10, cis-12 conjugated linoleic acid causes inflammation and delipidation of white adipose tissue in mice: a microarray and histological analysis
Physiol Genomics, November 21, 2006; 27(3): 282 - 294.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
K. Rogasch, V. Ruhmling, J. Pane-Farre, D. Hoper, C. Weinberg, S. Fuchs, M. Schmudde, B. M. Broker, C. Wolz, M. Hecker, et al.
Influence of the Two-Component System SaeRS on Global Gene Expression in Two Different Staphylococcus aureus Strains.
J. Bacteriol., November 1, 2006; 188(22): 7742 - 7758.
[Abstract] [Full Text] [PDF]


Home page
J Mol EndocrinolHome page
A. Petri, J. Ahnfelt-Ronne, K. S. Frederiksen, D. G. Edwards, D. Madsen, P. Serup, J. Fleckner, and R S. Heller
The effect of neurogenin3 deficiency on pancreatic gene expression in embryonic mice.
J. Mol. Endocrinol., October 1, 2006; 37(2): 301 - 316.
[Abstract] [Full Text] [PDF]


Home page
Infect. Immun.Home page
M. Lo, D. M. Bulach, D. R. Powell, D. A. Haake, J. Matsunaga, M. L. Paustian, R. L. Zuerner, and B. Adler
Effects of Temperature on Gene Expression Patterns in Leptospira interrogans Serovar Lai as Assessed by Whole-Genome Microarrays.
Infect. Immun., October 1, 2006; 74(10): 5848 - 5859.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
D. Abdueva, D. Skvortsov, and S. Tavare
Non-linear analysis of GeneChip arrays
Nucleic Acids Res., September 10, 2006; 34(15): e105 - e105.
[Abstract] [Full Text] [PDF]


Home page
Clin. Cancer Res.Home page
J. Fan and Y. Ren
Statistical Analysis of DNA Microarray Data in Cancer Research
Clin. Cancer Res., August 1, 2006; 12(15): 4469 - 4473.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
I. C. Gunesekere, C. M. Kahler, D. R. Powell, L. A. S. Snyder, N. J. Saunders, J. I. Rood, and J. K. Davies
Comparison of the RpoH-Dependent Regulon and General Stress Response in Neisseria gonorrhoeae
J. Bacteriol., July 1, 2006; 188(13): 4769 - 4776.
[Abstract] [Full Text] [PDF]


Home page
J. Immunol.Home page
M. H. Lahoud, A. I. Proietto, K. H. Gartlan, S. Kitsoulis, J. Curtis, J. Wettenhall, M. Sofi, C. Daunt, M. O'Keeffe, I. Caminschi, et al.
Signal Regulatory Protein Molecules Are Differentially Expressed by CD8- Dendritic Cells
J. Immunol., July 1, 2006; 177(1): 372 - 382.
[Abstract] [Full Text] [PDF]


Home page
J. Bacteriol.Home page
I. C. Gunesekere, C. M. Kahler, C. S. Ryan, L. A. S. Snyder, N. J. Saunders, J. I. Rood, and J. K. Davies
Ecf, an Alternative Sigma Factor from Neisseria gonorrhoeae, Controls Expression of msrAB, Which Encodes Methionine Sulfoxide Reductase.
J. Bacteriol., May 1, 2006; 188(10): 3463 - 3469.
[Abstract] [Full Text] [PDF]


Home page
Plant CellHome page
R. Schwab, S. Ossowski, M. Riester, N. Warthmann, and D. Weigel
Highly Specific Gene Silencing by Artificial MicroRNAs in Arabidopsis
PLANT CELL, May 1, 2006; 18(5): 1121 - 1133.
[Abstract] [Full Text] [PDF]



Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.