Sample A: Cover Page of Thesis, Project, or Dissertation Proposal

hybridization and multiple dye strategies, so the procedures developed in this research do not
handle this class of problems.
Gene Structure Factors
A probe covers only a small fraction of the possible target sequence, and the investigator should
be, but often is not, wary of drawing conclusions about the expression of the ‘gene’ that, in fact,
are true only for a particular isoform of the gene. Current chip designs are attempting to account
better for exon coverage and alternative transcript events across sample comparisons by
increasing the number of probes and diversifying their placement [9]. Isoform-sensitive analysis
does depend on an underlying gene model [43, 44]. While the results of the research presented
here are sensitive to probe position and gene models, the resolution of competing models requires
wet-lab methods not available to us, so the results shown present likely alternatives rather than
absolute outcomes.
Commonly Recognized Confounding Factors
The underlying goal of Microarray technologies is to detect and quantify biological compounds.
Any such molecular assay faces the sensitivity challenge of augmenting the signal of very rare
events, setting conditions that optimize the specificity of interactions, minimizing background
contributions, and respecting device limitations, ideally by including external and internal
calibration standards. To date, standard platforms for Microarray analysis have not focused on
robust and standardized wholesale technical solutions to these problems, but instead have focused
on one particular technical aspect in which to specialize (and segment from the competition) and
then relied on statistical methods embodied in algorithmic analysis pipelines for signal
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