The post tag might be inappropriate as this post mainly deals with Protein Structure Data, however the concept is similar to analyzing Differentially Expressed Genes.
I have two N dimensional row vectors of raw scores - S1 and S2, where the scores correspond to B factors of residues in the same protein. The vectors have same number of elements, say n1. As the scores in the vectors are computed using different methods, I converted the raw scores into standardized scores (Z scores) yielding vectors Z1 and Z2. The intention is to compare the two vectors of B factors and check for increase/decrease in fluctuation at each position.
I used the concept of Fold Change to compute the increase/decrease in fluctuation at each residue position. However, I got stuck in situations where one Z score is +ve and the other is -ve; e.g. when Z1(r=5) > 0 and Z2(r=5)<0. One possible way I thought of doing this was converting the Z score into positive scale (by adding the absolute minmum of the two vectors to the Z score vector). However, the issue then would be that the original ratio will not be retained as mentioned below.
[Z1(r=5)] + |m| / [Z2(r=5)] + |m| is not always equal to Z1/Z2. 'm' is the minimum value of the 2 vectors.