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

the energy of the excitation stage, but this raises the lower limit of detection to
unacceptable levels [39]. Using two excitation gains successively gives poor results
because of photo-bleaching of the dye and the non-linear relation between the gain
settings [38]. The effect of saturation is that the scanner makes a stochastic
estimation of the relative amount of fluorescence – although a numerical value is
supplied the true value should be ‘very big’ [59]. Scanner manufacturers provide
instrument specifications that supply the required sensitivity limits but no pipelines
make use of these values. Corrections for individual scanners could be found by the
use of either internal or external standards [38], but no ‘standard’ calibration reagents
are available, and indeed almost no one is aware of the problem. Most analysis
pipelines do enforce at least lower and sometime upper bounds on acceptable
measurement values, but these are typically arise from purely statistical assessments
of variance. The better strategy is to remove all data from the stochastic response
regions, as in done with ELISAs, and then look at the statistical variation of properly
quantified spots.
Microarray Platforms
Published reviews that describe Microarray experiments generally designate two categories:
oligonucleotide or cDNA probes [14, 15]. The difference in these array designs is the length of
the probe sequence and this difference arises from the production methods. The longer, cDNA,
probes are derived from either the excised inserts from clones or (usually) PCR products of those
inserts [15]. These probes range from 100 to 1000 nucleotides long and, because of their size
(length and tertiary structure), have limited spotting concentration and spot density [5]. Robotic
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