Microarray Platform Comparisons – Commentary on Barnes et al. (2005)

An extended analysis of the tissue dilution data generated by Barnes et al on the Affymetrix GeneChip® and Illumina® BeadArray platforms is presented in this white paper. Although the study is statistically underpowered, the authors, Barnes et al., conclude that the two platforms show comparable performance. However, their data demonstrates that the Affymetrix platform shows significantly greater reproducibility than the Illumina platform. A simple exploratory approach to the data highlights a clear difference in the ability of the two platforms to capture the underlying biology with the Affymetrix platform being significantly more effective. Statistical modeling of the data reveals clear differences in the signal/noise ratios for each platform; the Affymetrix and Illumina platforms exhibit signal/noise ratios of 8.19:1 and 1.20:1 respectively. As a direct result, the Affymetrix platform yielded 10 times more genes showing differential expression at a statistical significance of <0.05 when comparing the 5% Placenta (the lowest dilution) to 100% PBMC. Pathway analysis confirmed that the detected genes reflected the underlying biology and were not an artifact of the analysis approach. As a direct measure of the utility of each platform as a classification tool, the ability to reproducibly build classifiers with the data sets was tested. When presented with the most stringent sample set, the Affymetrix platform displayed a classification accuracy of 77% while the Illumina platform performed no better than random. With the understood statistical power limitation of this study design, these analyses suggest significant performance advantages to using the Affymetrix GeneChip system when studying real-life biological systems.