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

samples in the class, as well as the average ProbeSet intensity over the samples in the class, show
that there is remarkable consistency of the probe response profiles between experiments, some
examples of which are shown in Figure 2.5. ProbeSet responses across samples in a class were
further categorized based on the outcomes of Welsh’s T-tests [51], which were performed, per
probe, in log2 space with an alpha of 0.05. Each set was assigned to one of three categories,
described above as U, DE and S. Figure 5 shows examples of some of the results, giving side by
side comparisons. As can be seen, in the U class no significant differences in the class means
were found, while in the DE category the sets show significant differences (up or down) in the
class means. The S category may result in a ProbeSet mean value in either U or DE, depending on
the number and contribution to the total intensity of the individual probes in the set. The S
category of ProbeSets thus identifies specific transcript regions or probe–target interactions that
need additional analysis to be understood. Provided in the Supplementary Materials is the folder
ProbeLevel: within the folder are files consisting of 100 randomly selected ProbeSets per
classification category along with a random probe QQplot that demonstrates the T-test’s validity
in discriminating significant differences in this type of data.
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