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We explored other measures of probe performance from our array CGH data, including raw intensity measures for Cy3 (532 channel) and Cy 5 (635 channel) both separately and combined, and the ratio of the standard deviation to the mean intensity across experiments for Cy3, Cy5, and combined intensities.
For each individual, we calculated the mean intensity across the two cores.
This explains the variations in prevalence and geometric mean intensity across the different schools.
To exclude voxels susceptible to signal dropout, for each ROI, voxels with mean intensity (across timepoints) < 2 SD from the mean intensity (across voxels) in an ROI were removed from the ROI (Libby et al., 2012).
Probeset redundancy (where present) was reduced by identifying the probe with the highest mean intensity across all samples.
Within-array probe replicates were defined as technical replicates, by calculating the mean intensity across the different probes.
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Due to the high variability of the mean intensities across different SNP arrays, normalization is necessary to make different SNP arrays comparable [17].
On the other hand, a trend of growth in the standard deviation of mean estimates σ μ with increase of mean intensities across the dynamic range is not certain (in blue in Figure 1) and even σ μ = const cannot be excluded (the case of purely systematic error).
Here Maxchange is defined as the ratio of highest to lowest mean intensity observed across the cell line panel.
The level of expression of each probe set was centered on its mean intensity computed across all samples and logarithmically (base 2) transformed.
For each Affymetrix sequence (or probe set), log-ratio was defined to be the log10 of the intensity ratio of each animal (either treated with vehicle or CMP013) to the mean intensity of that sequence across the five profiles in the corresponding vehicle control group.
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