Comparison Between Affymetrix and Illumina Gene Expression Microarray Platforms

Abstract

<p>DNA microarray technology is an exploratory tool that can be used to measure thousands of gene expression values simultaneously. Many different microarray platforms have been developed. Various studies have shown that the same experiment performed in different laboratories using the same or different microarray platforms sometimes produce very different results. The lack of reproducibility is becoming a major challenge when comparing the microarray experiments across different labs and different platforms.</p> <p>Our study is focused on the cross-platform reproducibility between the Affymetrix GeneChip and Illumina BeadChip using two rodent experimental models for Type-1 diabetes. Within-platform reproducibility is also checked for the Illumina platform. Comparisons are carried between the two platforms in terms of the physical array features, the data quality and the chip effects, and finally the SAM analysis. Our study suggested that the overall comparability between these two platforms is fairly poor, however some findings are promising and the results show some agreement with the conclusions found in Barnes et al. (2005).</p>