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

position of the probe on the transcript, and the many ProbeSets that violate the [0-15] set criterion
for assignment of virtual position we do not consider this to be a serious lack of concordance. It
is possible that the result is due to a dye incorporation bias [59-61], or a cDNA conversion or
PCR amplification problem not assessable by this technique [36].
ProbeSet Assessment Results
Sample filtering excluded those samples which exceeded ±2 standard deviations of either the
average probe intensities or the number of contributing probes, at the probe level. The average
intensity per ProbeSet and the contributing number of ProbeSets per array were calculated and
graphed; the output is similar to what was shown in Figure 2.3 and these plots are provided in the
Supplementary Data, in the Filters folder. The ProbeSet number filter was the more stringent of
the two filtering steps, even with the exclusion boundary set to -1.5 standard deviations of the
mean ProbeSet number instead of 2. This selection was made purposely less stringent in order to
enrich the overall ProbeSet intersection prior to down-selection. The final sample numbers
remaining for the Bhattacharjee experiment were: 125 Adenocarcinoma, 13 Normal, 17
Squamous, 18 Pulmonary Carcinoma, and 5 Small Cell Carcinoma. The remaining sample
numbers in the Stearman experiment were: 17 Adenocarcinoma and 14 Normal.
Consistency of Probe Response
The last refinement in the cleansing process is to identify the intersection of common probes over
the samples: the x and y locations were used to identify matched probes across all of the
remaining samples. Next, sets containing at least 4 probes were collected, and from these the
ProbeSet mean intensities were calculated as the simple mean of the values of the probes
remaining in the set, for each sample. Graphical displays of the average probe intensity over the
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