A pair plot is a scatterplot of two samples, or two probes. The remainder of the discussion is framed in terms of a sample pair plot, but applies equally well to plots of probe pairs.
The individual (X,Y) points take their X value from the first sample and their Y value from the second sample.
The data is plotted on a logarithmic scale, and regression is done on log-transformed data.
A least squares line is fitted to the data, and the correlation coefficient reported.
If probes are selected, they will be highlighted in the probe table.
The mean deviation from the LSQ line is reported, both in log10, and as a coefficient of variation.
The CoV is defined as 10^(mean deviation). It signifies the average difference (as a ratio) for each point from the predicted line.
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