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The graph shows mean intensity, error bars indicate SD.
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Second, to refine the rigid registration, a quaternion-based rigid registration scheme was used, which minimizes the mean-squared intensity error by a gradient-descent optimizer.
The data were expressed as mean intensity ± standard error.
Figure 5 shows mean intensity ratios (MM/PM) with error bars corresponding to 95% confidence intervals, averaged over 60 PM probes and their cognate MM probes, from 10 arrays hybridized to a variety of samples.
The graphs show mean intensity of two independent experiments, the error bars indicate SEM.
To achieve a more stringent gene list we further filtered the 4,279 genes to remove weakly expressed genes (below 1.5 X the mean intensity of controls plus one standard error), and also removed genes with a fold-change below two.
A similar measure has been used in [58] called the absolute mean brightness error (AMBE) which measures the deviation of the mean intensity of the enhanced image (m c ) from the mean intensity of the original image (m o ).
Variance Stabilization [ 34] incorporates data calibration, an intensity-dependent error model and data transformation; it is intended to lead to a measure of differential expression which is independent of the mean intensity.
In prior benchmarking, the method has yielded affect intensity mean percentage errors of 5% or less on similar Dark Web forums [36].
To map intensities from different replicates onto similar scales without altering the absolute ratio values, we multiplied the intensity values on each array by a constant such that mean square error between the intensities of that array and the intensities of the first replicate array was minimized.
To work out the maximum embedding rate under various embedding intensities, the mean square error is still used as the transition.
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