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

and chip layout [64]. In particular, a master ‘.CDF’ file provides the cell definition, or array
design layout, while each sample has a corresponding .CEL file, or intensity output per spot file
[9]. The CDF file contains the essential information about the chip’s probesets: x and y spotting
locations for each probe, the index position of each probe, and each probe’s perfect match or
mismatch identity. The .CEL files are arranged by the x and y spotting locations and contain the
pixel size, signal intensity and standard deviation of the fluorescence across the pixels in the spot,
as extracted by Affymetrix’s scanner software.
Each probe has a Doppelgänger, a probe incorporating a deliberate mismatch, intended to provide
a non-specific hybridization observation [9]. Probes are designed to either have perfectly
matched the entire sequence or have substituted a mismatch nucleotide at the 13 th position in the
probe sequence (homomeric transversions: A ! T and G ! C). Originally the analysis software
from Affymetrix subtracted the MM signal from the corresponding PM signal [9]. The same
confounding issues for the perfect match sequences affect the mismatch sequences, although the
issue for these sequences is that cross hybridization and SNPs can now attenuate the background
correction and thereby potentially nullify the perfect match signal [65]. The confounding factors
have made the research community skeptical of the use of mismatch (PM-MM) subtractions and
by Affmetrix’s own admission, these mismatch sequences are rarely used [66]. There are 409,
600 probes on this U95Av2 array. In addition to the MM probes there exists an additional 3,935
manufacturing quality control probes, all of which lack rudimentary information such as id and/or
sequence. These probes apparently are used as controls in the manufacturing process but to the
data analyst represent black boxes into the Affymetrix software implementation of spot
assessment.
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