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

Table 2.4: ProbeSet behavior of probe level analysis. Number of ProbeSets in each response type, for each
experiment, and in common, following use of the BaFL protocol.. Note that the ‘informative’ category is
based upon the probe behavior within a ProbeSet, but for the Signal class the two groups may not agree as
to which probes in the set differ, a not unexpected outcome if transcript isoforms vary by individual
Bhattacharjee Stearman Intersect
Cleansed ProbeSets 4,253 6,506 4,200
Uninformative 2,810 1,233 1,225
Informative 1,443 5,273 1,219
Signal 1,288 4,536 937
DE 155 737 79
Transcript Regions Identified by Signal Probesets
Individually, there were 75 ProbeSets failing the statistical power test, 104 ProbeSets having
single probes in which a measurement issue, 18 ProbeSets conforming to the single transcript
region event criterion, and 128 ProbeSets suggesting distinct transcript region events. More
importantly, all 325 probes required additional analysis in order to understand the nature of the
information in the signal, and the BaFL approach allows the investigator to assess and prioritize
the ProbeSets to evaluate. In addition to identifying the rule under which particular classes of
probes were excluded, our method provides a category for sets containing probes with variable
behavior (some of which might have been excluded by the two statistical methods, depending on
cutoffs of variability chosen). To highlight why this is important we provide two specific
examples. For the two ProbeSets (1985_s_at and 39073_at) mapping to the NME1 gene, both
were categorized as Signal sets, where not every probe within the accepted probe-set is
differentially expressed, while a third ProbeSet that maps to the same gene (1521_at) is classified
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