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

Results
The results sections is divided into thirds, with the latent structure presented first as final
supporting evidence as to the quality of the BaFL-DE-intersection 325 ProbeSets. The next
section presents the analysis supporting the inclusion of SPP1, osteopontin, in the candidate list;
briefly, the ProbeSet was identified by the BaFL pipeline as being ‘on’ for the adenocarcinoma
and ‘off’ for the normal samples. Only two such on/off genes were identified in these data sets.
The final section shows the performance results of the candidate gene lists in independent
validation across the two datasets, where the BaFL interpretation is benchmarked against the
RMA and dCHIP interpretation for the same list of 31 candidate ProbeSets.
Latent Structure
Principal component analysis (PCA) of the latent structure of 325 candidate genes was performed
to project the genes into 2 dimensional space, based upon the correlation between samples. The
RMA and dCHIP algorithms center and scale their data to better approximate a normal
distribution, while the BaFL produced data is log transformed to achieve a similar approximation.
For all analysis the data was centered through the R functional parameter (center=T), although
scaling was not done (scale =F). Presented in Figure 4.1 is the PCA latent structure for the
Bhattacharjee dataset for the three sets of values.
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