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

do observe that the BaFL interpretation outperforms dCHIP and RMA, particularly if centering
and scaling the BaFL data further improves the classification accuracy, as we expect.
Table 3.2: Candidate list concordance numbers. Numbers of ProbeSets in candidate gene lists, starting
with the original list (column 2) with the filter of passing the BaFL filtering criteria (column3), and the
percentage of those (column 3) ProbeSets which show concordant differential expression classification
between datasets per cleansing methodology (last three columns).
List
Total
BaFL
retention
RMA dCHIP BaFL
% DE
Concordance
% DE
Concordance
% DE
Concordance
Bhatt
80% 675 267 54.68% 56.55% 31.46%
Bhatt
85% 366 136 58.09% 59.56% 36.76%
Stearman 409 178 92.13% 80.90% 44.94%
BaFL !
DE 325 325 92.62% 95.69% 100.00%
Conclusion
Although clustering and weighting schemes differ, in general the information content of a gene
with respect to phenotype is believed to be larger when it is significantly differentially expressed
and always in the same direction (i.e. up or down) across experiments. This many not be true for
multigenic interactions, or where an effect is due to a larger range of expression rather than a
particular level or direction of change, but most methods rely on the first assumption. It is true
that genes that are expressed but do not change are not at all informative. If the measure of
importance is linked to differential expression then the method that most consistently shows the
same genes changing under the experimental conditions, in the same direction and to the same
extent, will be a preferred method. The BaFL pipeline values have been shown in this chapter to
deliver this result. We note here that in this chapter we used the aggregated ProbeSet values, even
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