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[eulerian]

I just received a rejection email from the editor of a journal for my paper. What is puzzling, though, is the attached referee's report recommended publication of my paper in the journal.

The editor's email doesn't really explain, in my opinion, why he decided to reject my paper against the referee's recommendation, other than what it looks to me like a canned message "our journal receives so many wonderful papers that we have to reject many high-quality papers...." It is hard for me to figure out if he really means it in this case...

Should I email the editor and make sure that this is not a mistake or anything? I know that the decision ultimately lies in the editor not the referee and I can certainly live with whatever the outcome is. But, I am really wondering if there is any real reason why my paper is rejected, or, if they indeed receive so many great articles that they cannot publish all the ones with referee's positive recommendation. If I do email the editor, how I do it politely?

[croaker]

Editors don't have any obligation to follow reviewer guidance.  Often reviewers lack the "big picture" of what the journal is looking for or whether the contribution of a manuscript is sufficient for that particular journal.

However, it works both ways.  I have had a number of editors ignore the advice of reviewers to turn down my work.

The fact that someone liked your paper is a good sign.  Try to build on the comments you received and send it back out to another journal.

[onestep]

It's possible that  an internal review didn't find your paper compelling.  The reasons are many:  too similar to another paper; important issues missed by the reviewer; journal moving in another direction; tired of your topic; bad day in the editorial office. 

Additionally, reviewers are often asked to provide supplemental information not shown to the investigator.  For example, some journals ask the reviewers to rank papers on originality and validity on a score of 1-10.  It's possible that the journal has a policy of accepting papers that were both "accepted" and scored 10s.  The reviewer might have also included some qualifying information that was omitted in the review you received.

You might ask a mentor to look over the review and the editor's comments.  One of my colleagues thought she received a rejection letter when in fact it was a "revise and resubmit." 

That said, congrats on getting a good review.  I hope your paper gets accepted somewhere  soon!

[august_leo]

You might ask a mentor to look over the review and the editor's comments.  One of my colleagues thought she received a rejection letter when in fact it was a "revise and resubmit." 

I've seen that happen before too. Have you asked anyone to read it over?

[terpsichore]

The referee recommends; the editor decides. And even a recommendation to publish can have so little to say that it amounts to a non-recommendation.

Was there really only one referee? In that case, the editor may have done a second review personally.