How to respond to reviewer's comment that "magnitude of effect too small"? We received a decision letter of major revision recently. One of the four reviewers raised many comments like "Fig. XX, magnitude of effect too small." or "Fig. XX, scale condensed, magnitude of effect is very small", etc.

I have to say that the P-values are highly significant (P &lt; 0.001 in many cases) and our statistical analyses are solid as recognized by another reviewer in his or her comment. Although the absolute differences of measurement between two groups are quite small. The variation in each group is also very small. Therefore, if we quantify the magnitude of effect with effect size (a stanardized version of magnitude of effect), the effect size for the observed differences is medium of large based on the criteria here.

The reviewer has no specific comment about what we should do. How to respond to such comment properly?
I do not believe the reviewer is impugning the significance of your results. Instead, it sounds like the reviewer is suggesting that the scaling used on the graph makes it too hard to see the magnitude of the effects you're talking about. Perhaps he wants you to show a blown-up subset of the graph?