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

described above. In Figure 2.3, the top row presents the average probe intensities per probe
remaining in the cleansed array file (after removing values that fall outside the linear range). In
Figure 2.3, the bottom row shows the number of such probes remaining per array, with mean and
standard deviation lines provided for comparison. The arrays were grouped in the plots according
to their batch membership and are so labeled (‘X’ denotes batch 10; there is no batch 2 nor 9).
Batch 3 as a whole is skewed to the lower end in both tests, so the entire set of arrays was
removed from subsequent analyses. Since the probe sequence based filters remove exactly the
same probes in all cases, the difference as to which specific probes are removed between the
criteria is thus a result of the linear range filter. We believe that Batch 3 suffers from sample
degradation since the arrays demonstrate both lower average probe intensity and fewer overall
probes. In terms of the sample classes, the Normal samples (in red) were processed across several
batches and do not show markedly different overall responses than the disease samples in the
same batches.
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