Sample A: Cover Page of Thesis, Project, or Dissertation Proposal
Sample A: Cover Page of Thesis, Project, or Dissertation Proposal
Sample A: Cover Page of Thesis, Project, or Dissertation Proposal
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Figure 4.2: Non-traditional Laplacian dimension reduction. Results <strong>of</strong> the Laplacian dimension reduction<br />
method f<strong>or</strong> the Bhattacharjee data, showing ProbeSet c<strong>or</strong>relation by sample class. The direction <strong>of</strong> change<br />
<strong>of</strong> the ProbeSet is indicated both by col<strong>or</strong> and arrow. Latent structure is observed in all three groups. Top<br />
to bottom the graphs are from data matrices that started with values derived from the RMA, dCHIP, and<br />
log-transf<strong>or</strong>med BaFL values.<br />
The structure observed via the Laplacian dimension reduction method was assessed across both<br />
datasets to see if the structure was consistent in both. There was significant preservation <strong>of</strong> the<br />
structure in the case <strong>of</strong> the BaFL interpreted data, but in the RMA and dCHIP data sets the<br />
structure was lost, as presented in Figure 4.3. Statistical disc<strong>or</strong>dance indicates those ProbeSets<br />
which were found to be significantly expressed in only one <strong>of</strong> the datasets and applies only to the<br />
RMA and dCHIP produced values f<strong>or</strong> these 325 ProbeSets. Pattern disc<strong>or</strong>dance, on the other<br />
hand, indicates ProbeSets which demonstrated differential expression in both dataset, but the<br />
direction <strong>of</strong> change was different per dataset. While there does appear to be some latent structure<br />
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