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

Table 2.3: ProbeSet behavior predictions. Confusion matrices for classification of the informative nature,
comparing the classification of the predicted Lu probes and the observed BaFL cleansed Lu probes. TP is
true positive, FP is false positive. The first 3 confusion matrices show the result when t-test classification
is done at the probe level, while the bottom matrix is the equivalent comparison performed at the ProbeSet
level. ProbeSet level analysis was done for the predictive ProbeSets that are present in the cleansed Lu
output (True positive prediction rate for the presence of a ProbeSets was 91.64% and the False positive
error rate was 13.24% as shown in Table 2.2).
Level Confusion Matrix Class TP Rate FP Rate
Probe Level
Probe Level
Probe Level
3904 51 Noise
77 564 not Noise
540 79 Signal
55 3922 not Signal
18 4 DE
2 4572 not DE
ProbeSet Level 4444 13
Signal
DE
98.71% 12.01%
87.24% 1.38%
81.82% 0.04%
99.71% 6.47%
While the characteristic call may have a high level of sensitivity and specificity, as presented
above, the influence of a probe within a ProbeSet might either change the overall ProbeSet mean
expression and even the direction of relative expression (µ1 > µ2 ! µ1 < µ2), or make so minor
a contribution as to be irrelevant. To test the importance of such contributions, ProbeSet averages
were calculated for the probes predicted to be present in the Lu data, as derived from the BaFL
cleansed Bhattacharjee Stage I adenocarcinoma-squamous model. Similarly, the BaFL cleansed
ProbeSets were aggregated for the BaFL cleansed Lu dataset. Figure 2.7 shows the results of an
analysis, for the common ProbeSets, using fold change to summarize disease to normal
relationships, for the two sample types in the Lu dataset. The data generated by the BAFL
method demonstrates that the aggregation of the predictive individual probes closely mirrors that
of the BaFL cleansed probes for the Lu dataset. The consistency lies not only in selecting good
ProbeSets, but in handling the constituent probes correctly as well.
57