What to do if the editor's decision is not in your favor? I had recently developed a method and submitted as a manuscript to a journal. Out of four reviewers, three accepted the method and asked for some clarifications about the method:- 2 with major revision and 1 with a minor revision. But the left one,say X, has rejected and just written one line in his/her report i.e. "I feel the approach made in this method is not valid."

Editor's decision: Reject 

So I revisited all the approaches, discussed with  our group leader and co-authors. Our leader is advising to submit to other journal. But I would like to reply to X and the editor that my approach is quite valid. So how can I do it?

Is their anyone who is the superior to a editor?

Moreover, I am wondering how the editor took a negative decision just based on one reviewer's feeling? I would appreciate both the editor and reviewer, if they could have provided some hints why does the reviewer X feel this is not a valid approach.
You seem to assume that the editor rejected the article because of that one reviewer. That may be true, but my guess would be that that is not (entirely) the case. Reviewers just see one submission in isolation, the editor sees all the submissions, and only has limited space in her or his journal. So the editor typically cannot accept all articles that the reviewers thought were OK. Making that hard choice is her or his job. 

Given that and your description of what happened, it is extremely unlikely that any complaint procedure (if one exists for your journal) will be successful. 

Think of your options this way: such a procedure will take time, and during that time your article cannot be submitted somewhere else. So you loose time for a very small chance that it will appear in that journal. Alternatively, you could immediately submit is somewhere else, thus increasing the chance of getting published quicker. I know what I would do. 



Edit: Based on @Kay 's comments it seems clearer where the problem is. Kay seems to assume that the review process is a scientific debate. That premise is incorrect. Academic debates happen at conferences or after an article gets published. The peer review process is a mainly bureaucratic procedure aimed at quality control (with strengths and lots of weaknesses). The review process is not suited for an academic debate for (at least) two reasons: The anonymity makes it hard or impossible to directly respond, so there is no exchange, and the reviewer's main audience is the editor not the authors. The comments you get that help you improve your paper are basically a (very nice) side effect of that bureaucratic process, but the main aim is to help the editor decide whether or not (s)he wants to publish your article.