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

Figure 2.1: Batch images. Image representation of aggregated probe intensities per batch preparation. The
red circle depicts a localized feature, most distinct in Batch 10. Left 4 images: raw analysis of samples
meeting our filtering criteria. Right 4 images: the same samples with their cleansed probes averaged by
batch preparation and only common probes allowed. Probes affected by technical variation are eliminated
globally across all batches, including the ~5,600 from Batch 10.
Filter Effects
Since some of the filters lead to a considerable loss of the usable measurement pool, an obvious
question is the importance of any or all of the filters. Previously published work has shown the
effect that SNPs can have [11]. The largest subset of data is lost from the cross-hybridization
filter. It is unclear whether these potential probe-target duplexes form, and how much variation
can be expected across a sample population. To investigate this factor, an inversion of the cross-
hybridization selection query was performed, which produces a set of probes all of which may
cross-hybridize. If these probes are then subjected to all of the other filters we can isolate the
impact of this factor. Examples of the results are presented in Figure 2.2, showing how variable
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