Emerging Technology and Applications of Affymetrix GeneChips: Implications for Data Management and Analysis

Steve Lincoln

Surveys indicate that Bioconductor has emerged as one of the most commonly used environments for the analysis and quality control of data from microarrays in general, and from Affymetrix GeneChips in specific. Indeed Bioconductor is considered by most Affymetrix users to be both a proving ground and a gold standard for modern analysis methods. Of course, both current thinking in GeneChip data analysis, as well as the GeneChip technology itself, are rapidly evolving.

Using emerging manufacturing and instrumentation technologies which scale down to 5 micron features, cartridges with over 6 million different probes, as well as 96-well plates with 150 million probes, can be reliably manufactured, hybridized and scanned. In this very brief overview we will describe various new GeneChips which have be designed using these methods and will illustrate biomedical applications of these chips spanning the areas of gene expression, splice variant analysis, transcriptome analysis, genetic variation and copy number analysis. We will also provide a brief introduction to changes being implemented in the Affymetrix instrumentation and software to better accommodate the size and complexity of these data. These changes will also allow increased flexibility in analyzing GeneChip data using tools such as BioConductor.

We hope that this quick discussion will prove useful to Bioconductor developers in planning their own projects and collaborations. We also look forward to feedback from the Bioconductor community in all of these areas.