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

for the RMA and dCHIP interpretations, the separation is not complete as it is for the BaFL
results. Since, the latent structure that is presented by the BaFL interpretation could be an artifact
of normalizing the SVD matrix to the first ProbeSet, permutations were performed upon the
ProbeSet ordering. Permuting the gene order did not affect the latent structure that is observed,
although minor variations of the structure were found. These results are presented in the
Appendix E.
Figure 4.3: Cross dataset latent Laplacian structure. Results of the Laplacian dimension reduction method
on both the Bhattacharjee and Stearman data for ProbeSets, based upon sample correlations. These graphs
compare the 1 st Laplacian dimension of both datasets, Stearman on the y axis and Bhattacharjee on the x
axis. The direction of change is indicated by the color and direction of the arrow; there are four colors to
account for incongruencies in the direction of change between the datasets, as noted in the text. Latent
Structure is apparent in the third graph of the BaFL interpreted data. From top to bottom: RMA, dCHIP,
and BaFL produced values were used in the original data matrices.
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