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

filter acts as a PM only filter and if a mismatch adjustment is wanted then the investigator will
perform a preliminary analysis and incorporate this information into a modified CDF.
Sample Cleansing
Sample comparisons are usually performed prior to any data assessment, which can lead to
erroneous conclusions about which are the true outliers. We have presented a protocol that
proceeds via measurement characteristics to perform batch analyses for technical problems, and
follows up with probeset characteristics thereafter to manage biological outliers. The selection of
stringency is up to the needs of the investigator: when we relaxed the sample filtering process for
the Bhattacharjee adenocarcinoma versus normal samples, an additional 28 samples and
approximately 400 probesets were included, but the classification accuracy for the three
algorithms suffered (data not shown).
Platform Enabled Analysis Flexibility
Although not the primary focus of this report, the analysis platform we have used provides great
flexibility in selecting particular types of probes for detailed analysis. To produce the top half of
Figure 2.2 we selected only cross-hybridizing probes, to highlight how different the response
pattern they give is to the highly cleansed probes; to perform this analysis required that we alter a
single query. Another experiment identified which genes were considered present in the
adenocarcinoma state (minimum of 4 cleansed probes) and not present in the normal state (i.e. a
plus/minus analysis rather than relative expression analysis). This analysis identified osteopontin:
further investigation has shown that it has been implicated in lung cancer development and
patient survival [70-75].
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