Bioinformatics Vol. 19 no. 12 2003
Pages 1469-1476
© 2003 Oxford University Press
A comparison of statistical methods for analysis of high density oligonucleotide array data
Bioinformatics Sciences, GlaxoSmithKline Pharmaceuticals R&D, 709 Swedeland Road, King of Prussia, PA 19406-0939, USA
Received on November 25, 2002
; revised on February 27, 2003
; accepted on March 7, 2003
Motivation: Gene expression profiling has become an invaluable tool in functional genomics. A wide variety of statistical methods have been employed to analyze the data generated in experiments using Affymetrix GeneChip® microarrays. It is important to understand the relative performance of these methods in terms of accuracy in detecting and quantifying relative gene expression levels and changes in gene expression.
Results: Three different analysis approaches have been compared in this work: non-parametric statistical methods implemented in Affymetrix Microarray Analysis Suite v5.0 (MAS5); an error-modeling based approach implemented in Rosetta Resolver® v3.1; and an intensity-modeling approach implemented in dChip v1.1. A Latin Square data set generated and made available by Affymetrix was used in the comparison. All three methods—Resolver, MAS5 and the version of dChip based on the difference between perfect match and mismatch intensities—perform well in quantifying gene expression. Presence calls made by MAS5 and Resolver perform well at high concentrations, but they cannot be relied upon at low concentrations. The performance of Resolver and MAS5 in detecting 2-fold changes in transcript concentration is superior to that of dChip. At a comparable false positive rate, Resolver and MAS5 are able to detect many more true changes in transcript concentration. Estimated fold changes calculated by all the methods are biased below the true values.
Contact: dilip.2.rajagopalan{at}gsk.com
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  C. H. Seo, J.-R. Kim, M.-S. Kim, and K.-H. Cho Hub genes with positive feedbacks function as master switches in developmental gene regulatory networks Bioinformatics, August 1, 2009; 25(15): 1898 - 1904. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. J. Shaw, A. C. Ditewig, J. F. Waring, M. J. Liguori, E. A. Blomme, P. E. Ganey, and R. A. Roth Coexposure of Mice to Trovafloxacin and Lipopolysaccharide, a Model of Idiosyncratic Hepatotoxicity, Results in a Unique Gene Expression Profile and Interferon Gamma-Dependent Liver Injury Toxicol. Sci., January 1, 2009; 107(1): 270 - 280. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Deng, M. J. Liguori, E. M. Sparkenbaugh, J. F. Waring, E. A. G. Blomme, P. E. Ganey, and R. A. Roth Gene Expression Profiles in Livers from Diclofenac-Treated Rats Reveal Intestinal Bacteria-Dependent and -Independent Pathways Associated with Liver Injury J. Pharmacol. Exp. Ther., December 1, 2008; 327(3): 634 - 644. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Denoux, R. Galletti, N. Mammarella, S. Gopalan, D. Werck, G. De Lorenzo, S. Ferrari, F. M. Ausubel, and J. Dewdney Activation of Defense Response Pathways by OGs and Flg22 Elicitors in Arabidopsis Seedlings Mol Plant, May 22, 2008; (2008) ssn019v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 O. Ericsson, J. Jarvius, E. Schallmeiner, M. Howell, R. Y. Nong, H. Reuter, M. Hahn, J. Stenberg, M. Nilsson, and U. Landegren A dual-tag microarray platform for high-performance nucleic acid and protein analyses Nucleic Acids Res., May 1, 2008; 36(8): e45 - e45. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Chuchana, D. Marchand, M. Nugoli, C. Rodriguez, N. Molinari, and J. A. Garcia-Sanz An adaptation of the LMS method to determine expression variations in profiling data Nucleic Acids Res., May 14, 2007; 35(9): e71 - e71. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Kannangara, C. Branigan, Y. Liu, T. Penfield, V. Rao, G. Mouille, H. Hofte, M. Pauly, J. L. Riechmann, and P. Broun The Transcription Factor WIN1/SHN1 Regulates Cutin Biosynthesis in Arabidopsis thaliana PLANT CELL, April 1, 2007; 19(4): 1278 - 1294. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Deng, R. F. Stachlewitz, M. J. Liguori, E. A. G. Blomme, J. F. Waring, J. P. Luyendyk, J. F. Maddox, P. E. Ganey, and R. A. Roth Modest Inflammation Enhances Diclofenac Hepatotoxicity in Rats: Role of Neutrophils and Bacterial Translocation J. Pharmacol. Exp. Ther., December 1, 2006; 319(3): 1191 - 1199. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Makino, Y. Miyamoto, K. Sawai, K. Mori, M. Mukoyama, K. Nakao, Y. Yoshimasa, and S.-i. Suga Altered Gene Expression Related to Glomerulogenesis and Podocyte Structure in Early Diabetic Nephropathy of db/db Mice and Its Restoration by Pioglitazone. Diabetes, October 1, 2006; 55(10): 2747 - 2756. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. D. Coldren, B. A. Helfrich, S. E. Witta, M. Sugita, R. Lapadat, C. Zeng, A. Baron, W. A. Franklin, F. R. Hirsch, M. W. Geraci, et al. Baseline Gene Expression Predicts Sensitivity to Gefitinib in Non-Small Cell Lung Cancer Cell Lines Mol. Cancer Res., August 1, 2006; 4(8): 521 - 528. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Weng, H. Dai, Y. Zhan, Y. He, S. B. Stepaniants, and D. E. Bassett Rosetta error model for gene expression analysis Bioinformatics, May 1, 2006; 22(9): 1111 - 1121. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. J. Cortez, C. A. Lyman, S. Kottilil, H. S. Kim, E. Roilides, J. Yang, B. Fullmer, R. Lempicki, and T. J. Walsh Functional Genomics of Innate Host Defense Molecules in Normal Human Monocytes in Response to Aspergillus fumigatus Infect. Immun., April 1, 2006; 74(4): 2353 - 2365. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. F. Waring, M. J. Liguori, J. P. Luyendyk, J. F. Maddox, P. E. Ganey, R. F. Stachlewitz, C. North, E. A. G. Blomme, and R. A. Roth Microarray Analysis of Lipopolysaccharide Potentiation of Trovafloxacin-Induced Liver Injury in Rats Suggests a Role for Proinflammatory Chemokines and Neutrophils J. Pharmacol. Exp. Ther., March 1, 2006; 316(3): 1080 - 1087. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. J. Sullivan, T. H. Teal, I. P. Luttrell, K. B. Tran, M. A. Peters, and H. Wessells Microarray analysis reveals novel gene expression changes associated with erectile dysfunction in diabetic rats Physiol Genomics, October 17, 2005; 23(2): 192 - 205. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. H. Ahmed, R. Lutjens, L. D. van der Stap, D. Lekic, V. Romano-Spica, M. Morales, G. F. Koob, V. Repunte-Canonigo, and P. P. Sanna Gene expression evidence for remodeling of lateral hypothalamic circuitry in cocaine addiction PNAS, August 9, 2005; 102(32): 11533 - 11538. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. E. Rowland, A. M. Lichanska, L. M. Kerr, M. White, E. M. d'Aniello, S. L. Maher, R. Brown, R. D. Teasdale, P. G. Noakes, and M. J. Waters In Vivo Analysis of Growth Hormone Receptor Signaling Domains and Their Associated Transcripts Mol. Cell. Biol., January 1, 2005; 25(1): 66 - 77. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Ebrahimnejad, T. Streichert, P. Nollau, A. K. Horst, C. Wagener, A.-M. Bamberger, and J. Brummer CEACAM1 Enhances Invasion and Migration of Melanocytic and Melanoma Cells Am. J. Pathol., November 1, 2004; 165(5): 1781 - 1787. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Spielewoy, K. Flick, T. I. Kalashnikova, J. R. Walker, and C. Wittenberg Regulation and Recognition of SCFGrr1 Targets in the Glucose and Amino Acid Signaling Pathways Mol. Cell. Biol., October 15, 2004; 24(20): 8994 - 9005. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. E. Shima, D. J. McLean, J. R. McCarrey, and M. D. Griswold The Murine Testicular Transcriptome: Characterizing Gene Expression in the Testis During the Progression of Spermatogenesis Biol Reprod, July 1, 2004; 71(1): 319 - 330. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. R. Walker, A. I. Su, D. W. Self, J. B. Hogenesch, H. Lapp, R. Maier, D. Hoyer, and G. Bilbe Applications of a Rat Multiple Tissue Gene Expression Data Set Genome Res., April 1, 2004; 14(4): 742 - 749. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Broun, P. Poindexter, E. Osborne, C.-Z. Jiang, and J. L. Riechmann WIN1, a transcriptional activator of epidermal wax accumulation in Arabidopsis PNAS, March 30, 2004; 101(13): 4706 - 4711. [Abstract] [Full Text] [PDF]
|
|