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

Figure 2.4: Data processing comparisons. Boxplots (top row) and histogram densities (bottom row) of the
Bhattacharjee data: summary of batch intensities. The left most pair depicts the completely unfiltered data
set, including batch 3: note the obvious offset in batch 3 and the strong skew to the resulting distributions.
The middle pair is sample cleansed data, without any of the sequence-based probe filtering, as is used for
input to the RMA and dCHIP algorithms: here the skew remains significant but no batches are outliers.
The right column shows the output after both probe and sample cleansing methods are applied: note that the
distribution is more normal but the tails have been truncated. Also note that the total density scale on the
last plot is 10-fold less because so many fewer probes are included (even noise adds up).
In addition to the batch analysis presented in Figure 2.4, the affy package provides analyses that
are graphed as M versus A and RNA degradation plots. The M versus A plots further support the
evidence of a batch 3 effect and are provided in the Supplementary Material, in the Cleansing
folder. Conversely, the RNA digestion plot provides no evidence of what seems to be a
degradation occurring in batch 3, but given the lack of correspondence between the index and
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