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

Figure 2.2: Confounding effects. The top 2 rows show the result of selecting cross- hybridizing probes
only (other factors still excluded). The bottom 2 rows present ProbeSets in their entirety: at each position
the confounding factor is indicated by the symbol (X = cross-hybridization and S = SNP). The binding
patterns of these probes (rows 1 and 2) vary considerably between experiments and sample classes. For
37298_at, in the fourth row, we observe that while in this case the cross-hybridization effect is not very
strong, especially if averaged into a ProbeSet, 4 of the 5 SNP afflicted probes will produce significant
differences in the averages between the experiments regardless of sample class. Probe index 8 for 37298_at
(fourth row) failed to meet the linear range criterion in some of the samples (the solid line at 200 f.u.): it
also shows cross-hybridization but is omitted from the top row because the other filter also applies. The
values for a probe across the sample in the class were averaged to achieve the value shown. Parallel sets of
probes, for the two independent experiments, are shown side by side.
Array-Batch Results
Arrays that are outliers due to sample processing problems were identified by comparing
individual arrays to the batch-mean values within each experiment. Technical problems are
assumed to manifest themselves by increased variance at the measurement level, the tests are
46