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