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Multiple-laboratory comparison of microarray platforms

A Corrigendum to this article was published on 01 June 2005

Abstract

Microarray technology is a powerful tool for measuring RNA expression for thousands of genes at once. Various studies have been published comparing competing platforms with mixed results: some find agreement, others do not. As the number of researchers starting to use microarrays and the number of cross-platform meta-analysis studies rapidly increases, appropriate platform assessments become more important. Here we present results from a comparison study that offers important improvements over those previously described in the literature. In particular, we noticed that none of the previously published papers consider differences between labs. For this study, a consortium of ten laboratories from the Washington, DC–Baltimore, USA, area was formed to compare data obtained from three widely used platforms using identical RNA samples. We used appropriate statistical analysis to demonstrate that there are relatively large differences in data obtained in labs using the same platform, but that the results from the best-performing labs agree rather well.

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Figure 1: Precision and accuracy assessment figures.
Figure 2: Plots demonstrating agreement for differentially expressed genes.
Figure 3: Venn diagram illustrating agreement between annotation databases.
Figure 4: CAT plots showing agreement in differential expression calls, based on fold change, between each lab and a reference lab.

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Acknowledgements

We thank A. Nones and K. Broman for useful suggestions. The work of R.A.I. is partially funded by the National Institutes of Health Specialized Centers of Clinically Oriented Research (SCCOR) translational research funds (212-2494 and 212-2496). The work of G. Germino and I. Kim was partially funded by NIDDK U24DK58757.

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Correspondence to Rafael A Irizarry.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Observed log fold change versus RT-PCR log fold change for the four altered genes and 12 selected genes. (PDF 672 kb)

Supplementary Fig. 2

Preprocessing effect. (PDF 1279 kb)

Supplementary Fig. 3

SD (measure of precision) plotted against experience of technician for each of the five Affymetrix labs. (PDF 453 kb)

Supplementary Fig. 4

Precision assessment for the new Affymetrix chip. (PDF 525 kb)

Supplementary Table 1

Within and across lab assessment measure comparing preprocessing procedures as for Supplementary Figure 2. (PDF 52 kb)

Supplementary Table 2

Effect of annotation on across-lab agreement. (PDF 59 kb)

Supplementary Table 3

Across-lab agreement. (PDF 61 kb)

Supplementary Table 4

Assessments for results from lab 5 using old and new chip compared to results from the best performing labs. (PDF 48 kb)

Supplementary Methods (PDF 67 kb)

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Irizarry, R., Warren, D., Spencer, F. et al. Multiple-laboratory comparison of microarray platforms. Nat Methods 2, 345–350 (2005). https://doi.org/10.1038/nmeth756

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