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Comp Funct Genomics. 2005 Apr; 6(3): 116–122.
PMCID: PMC2447518

Meta-Analysis Combines Affymetrix Microarray Results Across Laboratories


With microarray technology becoming more prevalent in recent years, it is now common for several laboratories to employ the same microarray technology to identify differentially expressed genes that are related to the same phenomenon in the same species. Although experimental specifics may be similar, each laboratory will typically produce a slightly different list of statistically significant genes, which calls into question the validity of each gene list (i.e. which list is best). A statistically-based meta-analytic approach to microarray analysis systematically combines results from the different laboratories to provide a single estimate of the degree of differential expression for each gene. This approach provides a more precise view of genes that are of significant interest, while simultaneously allowing for differences between laboratories. The widely-used Affymetrix oligonucleotide array and its software are of particular interest because the results are naturally suited to a meta-analysis. A simulation model based on the Affymetrix platform is developed to examine the adaptive nature of the meta-analytic approach and to illustrate the utility of such an approach in combining microarray results across laboratories.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Choi Jung Kyoon, Yu Ungsik, Kim Sangsoo, Yoo Ook Joon. Combining multiple microarray studies and modeling interstudy variation. Bioinformatics. 2003;19 (Suppl 1):i84–i90. [PubMed]
  • Cui Xiangqin, Churchill Gary A. Statistical tests for differential expression in cDNA microarray experiments. Genome Biol. 2003;4(4):210–210. [PMC free article] [PubMed]
  • DerSimonian R, Laird N. Meta-analysis in clinical trials. Control Clin Trials. 1986 Sep;7(3):177–188. [PubMed]
  • Gautier Laurent, Cope Leslie, Bolstad Benjamin M, Irizarry Rafael A. affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004 Feb 12;20(3):307–315. [PubMed]
  • Ghosh Debashis, Barette Terrence R, Rhodes Dan, Chinnaiyan Arul M. Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer. Funct Integr Genomics. 2003 Dec;3(4):180–188. [PubMed]
  • Moreau Yves, Aerts Stein, De Moor Bart, De Strooper Bart, Dabrowski Michal. Comparison and meta-analysis of microarray data: from the bench to the computer desk. Trends Genet. 2003 Oct;19(10):570–577. [PubMed]
  • Parmigiani Giovanni, Garrett-Mayer Elizabeth S, Anbazhagan Ramaswamy, Gabrielson Edward. A cross-study comparison of gene expression studies for the molecular classification of lung cancer. Clin Cancer Res. 2004 May 1;10(9):2922–2927. [PubMed]
  • Rhodes Daniel R, Barrette Terrence R, Rubin Mark A, Ghosh Debashis, Chinnaiyan Arul M. Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res. 2002 Aug 1;62(15):4427–4433. [PubMed]
  • Rhodes Daniel R, Yu Jianjun, Shanker K, Deshpande Nandan, Varambally Radhika, Ghosh Debashis, Barrette Terrence, Pandey Akhilesh, Chinnaiyan Arul M. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A. 2004 Jun 22;101(25):9309–9314. [PMC free article] [PubMed]
  • Wang J, Coombes KR, Highsmith WE, Keating MJ, Abruzzo LV. Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies. Bioinformatics. 2004 Nov 22;20(17):3166–3178. [PubMed]

Articles from Comparative and Functional Genomics are provided here courtesy of Hindawi Publishing Corporation


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