How should irrelevant comment(s) from a peer reviewer be handled?

Some times an irrelevant comments is made on a peer review report based on which a paper is rejected and that makes the author very discouraging. Like "Proper discussion is not made why apple is red" while the paper is on lily flower. The answer could be any of the same
a) The editorial board should take care of such comments and provide the full support to evaluate the paper a s per merit rather than rejection.
b) The paper be rejected and resubmitted to the same or other Journal citing the rejection cause.
c) The author should write a strong letter to the chief editor to black list such reviewers and request evaluate the paper as per merit.
d) The publisher also have some responsibility as it may raise an anti-publisher X waive among the authors. 
e) Such sensitive matter be discussed in an open international platform combing all publishers and impartial judges to take decision on the matter.

Analytical toxicology Aquatic toxicology Biochemistry Bioinformatics Biomarkers
 Игнорировать и делать по своему если уверен в своих данных. Но учесть замечания 
в последующей работе.
Rolf Teschke
This issue should be discussed with the editor.

Sanka Niranjan Atapattu
What you mention is quite common, especially when a manuscript goes to reviewers who do not have the background to understand your research work. If your paper is rejected, I think the most practical thing to do is submit it to another journal whose aims and scope are within your manuscript. 
In my oppinion, the author can politely write the editor proving his case with strong justification(s) and calling the attention of the editor about such comment. Sometimes, the editors are too busy with many papers, they might not notice such misleading comment from the reviewer. Authors should know that they can always challenge or rebut some review comments if they have strong justification.
This is simple.
A) If the Editor was writing to you that rejections was due to the argument that "why the apple is red" is not discussed: Then you are free to approach the Editorial Board i.e. the Editor and the EiC for reassessment (and this usually works very well if done polite and convincing). There you need to argue scientifically why red apples are not related to lily flowers, and ask for reevaluation of your (revised) submission (including revision addressing all purposeful comments and an accompanying letter). 
B) If the editor named other arguments of rejection (while the referees was dabating also the red apple): Often this does cause angriness; and you will understand better once calming down from the initial frustration. Then think about these concerns and accept the rejection. Next is to substantiate the manuscript against the concerning issues (if you can). Usually you have to send it somewhere else (after rejection) unless the "previous" Editor was allowing an extensively reworked manuscript as new submission (i.e. new peer-review, usually different referees).
C) The Editor did reject your submission without giving an argument other then forwarding the referee comments: That is a badly managed Journal. Bad luck for you. Seek for a more professional one that has useful SOPs to support scientific publishing.
I think the best decision is to resubmit your manuscript to another Journal considering comments of reviewer(s). There are many possibilities for this and author(s) will certainly find suitable Journal. Although I had to review manuscripts which hardly could be published in any Journal.
 In any case, rejections are to be based on proper explanations and simplifications. The author should know what were the main reasons for being rejected.
      Each one of us, including people from all professions, should take rejection as a natural part of life and career  advancement.

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