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

Figure 2.6: Probe-Transcript regions of interest. Examples from the 325 ‘Signal’ ProbeSets, which
aggregated as ‘DE’. The red boxplots are the adenocarcinoma samples (T) and the normals are in blue (N);
average p values are provided below the x-axis label. Probes of interest are indicated with the green brace.
Clockwise from upper left: 37047_s_at the 3 rd probe in the probe-set failed to demonstrate significant
difference in means, nor the pseudo-pattern inversion, suggesting that the difference is a matter of statistical
importance. The second probe of 32052_at demonstrates stronger evidence of a transcript event; however
an absence of neighboring probes complicates the analysis. The first 2 probes and second to last probe in
37028_at demonstrate 2 distinct regions worthy of additional analysis. The example probe 1985_s_at
demonstrates the aforementioned 3 (center) probes as a single transcript region displaying transcript
isoform phenomena.
A Priori Prediction
The Bhattacharjee data [47] cleansed via the BaFL pipeline was able to predict the sources of
variability in the third Lu dataset [33]; this demonstrates that this is a more robust approach to
probe cleansing, rather than either dChip or RMA, which offer no such ability. Presented in
Table 2.2 are the true positive and false positive prediction rates for the prediction that a probe
55