How to communicate with reviewer who has waived his anonymity?

Question

(Within the standard review process) I received review comments on a paper, one of the reviewers, say A, waived his anonymity in the review submitted to the journal (I know A personally). Now, A made some suggestions (essentially about some way of using software developed by students of A) which do not work (suggested feature does not exist). Should I

• write an email to A directly asking about clarifications on how to use the software as he suggested, at the risk of the handling editor feeling like I went behind his back
• write this email, but include the handling editor as CC:, at the risk of A feeling like I would "belittle" him "in front of" the editor, or
• mention in the response that the feature was not implemented in the suggested software, citing documentation / error messages

Answer 1

No matter what, I would suggest keeping all formal communications and responses within the journal system, even though the reviewer has waived anonymity. That way, you keep a clear record both for yourself and the editor but also for the other anonymous reviewers (if the journal shares reviews between reviewers as many do) and for any other journal staff who might later need to audit the interaction.

Now, given that the reviewer has revealed themselves, you may or may not find it appropriate to communicate informally about concerns that you may have. If the journal has approved the waver of anonymity (e.g., by the identity being revealed in the review that you were sent), then it's definitely OK. If it's come through a side-channel, however, then some might consider it fine (e.g., "anonymity is just to protect reviewers") and some might consider it unethical (e.g., "talking to your friend gives an unfair advantage").

Answer 2

It would not be appropriate for the reviewer to contact you before the review is submitted, but it doesn't seem to be the case here.

I would send a note back to A, thanking him/her for the suggestions and saying I would look in to it as you revise. You don't need to make any commitment nor to actually take the advice. The paper is yours. The editor will have a say when you submit any future version.

But do take a hard look at the advice. Maybe there is a germ of truth in what is said and that caused the reviewer to reach out. Maybe not.

If it is later reviewed by the same person who then objects to your not taking the advice offered you can complain to the editors at that point. There is no need to raise any issue now.