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

four assays is given in the second column of Table 3.1. That is, the first input gene list, ALL, is
the complete set of 12,625 ProbeSet values generated by RMA for the Stearman samples. The
second input gene list includes those 5,291 ProbeSets identified as being differentially expressed
in the Stearman sample, the third input gene list includes those 6,595 ProbeSets identified as
differentially expressed in the Bhattacharjee dataset and the fourth candidate gene list has the
3,761 genes identified as being in the intersection of the second two lists. The second row of
graphs uses the ProbeSet values generated by dCHIP, which are different from those given by
RMA, and this leads to somewhat different candidate gene lists (see Figure 3.7 in the Discussion
for more details) but follows the same pattern of assays, with the numbers given in Column 3 of
Table 3.1. The third row of graphs requires more description because the ‘complete’ matrix of
ProbeSet values generated by the BaFL pipeline does not include all of the possible ProbeSets,
unlike those of RMA and dCHIP, and therefore care must be taken that the same genes are
present in both the training and test data sets – in this case the number of input ProbeSets is given
in the fourth column of Table 3.1.
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