Calculate difference between two signals

What and how would be the best way to calculate the difference between the 2 signals (A and B) shown below in terms of percentage difference or a factor of comparison?

Answer 1

[Star Strider]

I would compare them by noting that the amplitudes of the peaks vary with respect to the independent variable, similarly for both ‘A’ and ‘B’. One way would be to do a simple linear regression of one against the other:

P = [A(:) ones(size(A(:)))] \ B(:)                  % P(1) = Slope, P(2) = Intercept

another would be to regress both of them with respect to the independent variable (assumed here to be ‘x’):

Pa = [x(:) ones(size(x(:)))] \ A(:)                  % Pa(1) = Slope, Pa(2) = Intercept
Pb = [x(:) ones(size(x(:)))] \ B(:)                  % Pb(1) = Slope, Pb(2) = Intercept

A direct point-by-point difference or a single statistic (for example mean of the difference between them) would not capture their both changing over the independent variable at different rates, and with respect to each other.