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

Probes are the complementary strands intended to hybridize to these targets, and are designed
against sequence databases of the genes of interest; chemical synthesis may occur on the array
surface (as for Affymetrix arrays) or occur first and then be subsequently attached at specific
positions [5]. There is no fixed limitation on probe length, and indeed the probes on an array may
differ slightly in length, if a melting temperature has been the defining parameter in the design
process [10]. Arrays are typically divided into short oligo and long oligo categories, and cDNA
arrays. Commercial vendors currently offer oligonucleotide-based arrays, ranging from 24-mers
[11] and 25-mers [8] to 70-mers [12], while cDNA arrays (usually, in fact, the PCR product of
cDNA inserts) were prevalent in the 1990s and early 2000’s [2, 13-15].
The difficulties inherent in interpreting cDNA data have led to a considerable drop in the number
of publications that use this style of array but they typically had much longer probes, usually
100+ nucleotides [15]. Each probe design strategy has its own individual merit with respect to a
particular experimental goal [14, 16], but the short oligonucleotide platforms are the most flexible
[10] and, as costs have decreased, have become the most prevalent in published scientific
literature.
Target mixtures are applied to the array surface and, after sufficient hybridization time and
removal of non-specifically bound material, the elicitation/capture of the signal molecule occurs
[10]. For fluorescent dyes this requires laser excitation of the dye in an imager or scanner with
sufficient resolution to separate the spots [5, 14]. From these pixel-by-pixel scanner
measurements an overall fluorescence per spot provides a qualitative representation of each
gene’s relative abundance [14]. A common assumption is that the intensity of the spot correlates
to the concentration of the original mRNA, directly and consistently across all spots. However, as
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