Consider a sample consisting of  observations (for example, objects of unknown volume).  Both assays (for example, different methods of volume measurement) are performed on each sample, resulting in  data points.  Each of the  samples is then represented on the graph by assigning the mean of the two measurements as the -value, and the difference between the two values as the -value.
The Cartesian coordinates of a given sample  with values of  and  determined by the two assays is
For comparing the dissimilarities between the two sets of samples independently from their mean values, it is more appropriate to look at the ratio of the pairs of measurements. Log transformation (base 2) of the measurements before the analysis will enable the standard approach to be used; so the plot will be given by the following equation:
This version of the plot is used in MA plot.