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

Probe Filtering Output
The probe sequence-specific filters remove unidentifiable targets, cross-hybridization sources,
and probes no longer matching targets, probes having limited duplex accessibility or stability, and
those probes for which the presence of SNPs is known. These filters are consistent across all
arrays; the independently excluded probe numbers for each filter are presented in Table 2.1. Also
presented in Table 2.1 is the total number of excluded probes when the filters are run
independently. As discussed above, the ordering of these filters is inconsequential to the final
outcome, although some probes may be removed for more than one reason, so the class in which
they fall will depend on the order in which the steps are run. The final x and y information for the
probe sequences belonging to the intersection of the cleansed ProbeSets is provided in the
Supplementary Data, as IntersectionXY.csv. We expect that the linear range limits are the
parameters most likely to be changed by other investigators, depending on the type of platform
and individual instrument behavior. We have some preliminary evidence that the proper setting
of the lower limit can be inferred from the measurement data (shown in the Supplementary Data),
but upper limits are more difficult to estimate, and in the absence of calibration standards
investigators must continue to rely on the instrument specifications.
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