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Attachment 2. Comparison of Microarray Data from Multiple Labs and Platforms
Pages 49-57

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From page 49...
... This technology promises to be a useful tool to better understand the role of genetics in biologic responses to environmental contaminants. Various examples were presented in the 10th Meeting of the Committee on Emerging Issues and Data on Environmental Contaminants.
From page 50...
... 50 Validation of Toxicogenomic Technologies studies have been published comparing competing platforms with mixed results: some find agreement (Kane et al. 2000; Hughes et al.
From page 51...
... Comparison of Microarray Data from Multiple Labs and Platforms 51 Furthermore, in my opinion, previous studies had at least one of these problems: (1) precision/accuracy were not properly assessed (that is, the sensitivity/specificity trade-off was not considered and in general, assessments were based on validation of few genes)
From page 52...
... 52 Validation of Toxicogenomic Technologies in microarray technology there exists a strong probe or spot effect. The Nature Methods publication (Irizarry et al.
From page 53...
... RESULTS Our results demonstrated that precision is comparable across platforms. With the exception of one lab, all the labs performed similarly, and it is clear that the lab effect is stronger than the platform effect.
From page 54...
... 54 Validation of Toxicogenomic Technologies 40%. Figure 2-2 plots the expected agreement of two bivariate normal random variables against their correlation.
From page 55...
... Comparison of Microarray Data from Multiple Labs and Platforms 55 FIGURE 2-3 Precision versus years of experience for labs using Affymetrix microarrays. Source: Irizarry et al.
From page 56...
... 2003. Spotted long oligonucleotide arrays for human gene expression analysis.
From page 57...
... 2002. Differential gene expression patterns revealed by oligo-nucleotide versus long cDNA arrays.


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