When to Assume vs. When to Ask

By Dr. Zubair Khalid, DVM, MS, PhD · 2026-08-28

Quick Answer

• Decide based on comment specificity: ask when the request is ambiguous, assume when the instruction is clear and you can verify your interpretation against the manuscript.
• Use the decision tree below to weigh misinterpretation risk against revision timeline before drafting your response letter.
• A key limitation is that no single rule fits every journal, so check the journal's specific revision guidance when it exists.

Understanding the Reviewer Comment Problem

Peer review comments arrive in many forms. Some are direct requests, such as "please add a power analysis" or "clarify how you handled missing data." Others are vague, such as "this section needs work" or "the methods are unclear." The challenge for researchers is deciding when to make an educated guess about what the reviewer wants and when to ask for clarification.

The cost of guessing wrong is a second round of revisions, delayed publication, and potential frustration from reviewers who feel their concerns were not addressed. The cost of asking too often is appearing unresponsive or creating unnecessary back-and-forth that slows the process. Neither outcome serves the author, the reviewer, or the journal.

This article presents a practical decision framework based on comment specificity, the risk of misinterpretation, and the revision timeline. The framework draws on publication ethics guidance and research reporting standards to help authors make defensible choices.

At a Glance

Core Principles for Responding to Reviewers

Understand the Purpose of Peer Review

Peer review exists to improve the quality and integrity of published research. The Committee on Publication Ethics Core Practices describe peer review as a process that journals should operate fairly and transparently. Reviewers volunteer their time to assess the validity of methods, the soundness of conclusions, and the clarity of reporting. When you receive comments, you are participating in a system designed to strengthen your work before it enters the public record.

This context matters because it shapes how you should interpret comments. A reviewer who asks for a change is usually trying to make the paper better, not to test your patience. Even when a comment seems off base, the reviewer is signaling that something in the manuscript is not clear enough for them to evaluate. Your job is to determine whether the problem is in the manuscript or in the reviewer's reading.

Distinguish Comment Types

Reviewer comments fall into several categories. Some are requests for additional analysis. Some are requests for clarification of existing text. Some are suggestions for restructuring. Some are questions about the study's limitations. Some are corrections of factual errors. Some are stylistic preferences.

The decision to assume or ask depends on which category the comment falls into and how specific the language is. A comment that says "please report the confidence intervals for the primary outcome" is a direct request. A comment that says "the results section is confusing" is a signal that something is wrong, but it does not tell you what to fix.

Recognize the Role of the Editor

The editor is the intermediary between you and the reviewer. When you submit a revision, the editor reads your response letter and decides whether the revision addresses the concerns. If you are uncertain about a comment, the editor is the appropriate person to ask. The editor can clarify what the reviewer meant or can make a judgment about whether your interpretation is acceptable.

The Committee on Publication Ethics Core Practices emphasize that editors are responsible for the overall quality of the peer review process. This means editors have a duty to help authors understand what is being asked. You should not hesitate to contact the editor when a comment is genuinely unclear.

The Decision Framework

Step 1: Assess Comment Specificity

Read the comment carefully and ask whether it names a specific element of your manuscript. A specific comment names a section, a variable, a statistical test, a figure, or a table. An unspecific comment describes a general problem without pointing to a location or a solution.

Specific comments usually warrant an assumption. If the reviewer says "the methods section does not describe how you handled outliers," you know exactly what to add. You can check your methods section, find the gap, and write the missing description. The risk of misinterpretation is low because the reviewer told you what they want.

Unspecific comments require more judgment. If the reviewer says "the discussion is not convincing," you have to decide what is not convincing. The reviewer might mean the interpretation is overreaching, the limitations are not acknowledged, or the comparison to prior work is weak. Each interpretation leads to a different revision.

Step 2: Evaluate the Risk of Misinterpretation

When a comment is unspecific, estimate the risk that your interpretation will miss the reviewer's intent. Consider the consequences of guessing wrong. If the wrong guess means you revise the wrong section, you will need another round of revisions. If the wrong guess means you change the study's conclusions, the risk is much higher.

The risk assessment should also consider the reviewer's likely tolerance for follow-up questions. Some reviewers are happy to clarify. Others expect authors to use their judgment. The journal's culture and the editor's style matter here, but you cannot know these in advance. The safest approach is to ask when the risk of misinterpretation is high and the cost of guessing wrong is substantial.

Step 3: Consider the Revision Timeline

Journals typically give authors a deadline for revisions. The deadline may be two weeks, a month, or longer. Your decision to assume or ask should account for the time available.

If you have a short deadline, asking for clarification may be impractical. The editor may not respond quickly enough for you to incorporate the answer. In that case, you may need to make your best interpretation and document it clearly in the response letter. If you have a longer deadline, asking is more feasible.

The revision timeline also affects how you structure your response letter. If you are making assumptions, you should state each assumption explicitly so the reviewer can see what you did and why. This transparency reduces the chance that the reviewer will think you ignored their comment.

Step 4: Decide and Document

Once you have assessed specificity, risk, and timeline, make your decision. If you assume, implement the change and explain your interpretation in the response letter. If you ask, send a concise question to the editor, not to the reviewer directly. The editor will relay your question or answer it themselves.

Documentation is essential. Your response letter should list every comment and your response. For each comment, state whether you made a change, why you made the change, and where the change appears in the revised manuscript. If you chose not to make a change, explain why. The Committee on Publication Ethics Core Practices emphasize transparency in the publication process, and a clear response letter is part of that transparency.

Practical Implementation Steps

Step 1: Read All Comments Before Responding

Read the entire set of comments from all reviewers before you start making changes. This gives you a full picture of what is being asked. Sometimes one reviewer's comment clarifies another reviewer's concern. Sometimes two reviewers ask for the same thing, which signals a genuine problem in the manuscript.

Step 2: Categorize Each Comment

Create a table with columns for the comment, the reviewer number, the comment type, the specificity level, and your proposed action. This table becomes the skeleton of your response letter. It also helps you see patterns across reviewers.

Step 3: Verify You Can Implement the Request

For each comment you plan to assume, check that you have the data, the analysis, or the text needed to implement the change. If you cannot verify the request, you may need to ask. For example, if a reviewer asks for a subgroup analysis and you do not have the subgroup variable, you cannot assume the request. You must either explain why the analysis is not possible or ask the editor how to proceed.

Step 4: Draft the Response Letter

Write the response letter in a structured format. Number each comment and provide a response beneath it. State clearly whether you made a change, what the change was, and where it appears in the revised manuscript. If you are asking for clarification, state that you are asking and why.

Step 5: Submit and Follow Up

Submit the revision and the response letter through the journal's submission system. If you asked a question, follow up with the editor if you do not receive a response within a reasonable time. The journal's instructions may indicate how long the editor will take to respond.

Records and Measurements

What to Track

Keep a record of every comment and your response. This record is useful if the manuscript goes through multiple rounds of revision. It also helps you identify patterns in how reviewers respond to your work, which can improve your future writing.

The record should include the comment text, the reviewer number, the date you received the comments, the date you submitted the revision, and the outcome of the revision. If you asked a question, record the question and the editor's response.

How to Measure Success

The primary measure of success is whether the manuscript is accepted for publication. A secondary measure is whether the reviewer's concerns are resolved in the first round of revision. If you receive a second round of comments, review your response letter to see whether the new comments address the same issues or new ones. If the same issues recur, your interpretation of the original comments may have been wrong.

Common Failure Patterns

One common failure is assuming when the comment is too ambiguous. The author makes a change that does not address the reviewer's concern, and the reviewer repeats the comment in the next round. This wastes time and can create the impression that the author is not listening.

Another failure is asking when the comment is clear. The author sends a question to the editor about a comment that was already specific. This can make the author appear unprepared or unwilling to do the work.

A third failure is not documenting assumptions. The author makes a change based on an interpretation but does not explain the interpretation in the response letter. The reviewer cannot see the reasoning and may think the author ignored the comment.

A fourth failure is ignoring the editor's role. The author asks the reviewer a question directly, which is not the standard process. The reviewer may not respond, or the editor may be annoyed that the author bypassed the journal's process.

Common Failure Patterns

The Over-Assumption Pattern

This pattern occurs when the author assumes the reviewer wants a specific change, but the reviewer's comment was vague. The author spends time making a change that does not address the reviewer's concern. The reviewer returns the manuscript with the same comment, and the author must start over.

The cause is usually a desire to avoid asking for help. The author may feel that asking a question shows weakness or incompetence. In reality, asking a well-formed question shows that the author is thinking carefully about the review.

The Over-Asking Pattern

This pattern occurs when the author asks for clarification on every comment, even the ones that are clear. The editor receives a long list of questions, many of which have obvious answers. The editor may become frustrated, and the revision process slows down.

The cause is usually anxiety about getting the revision wrong. The author wants to be certain, but the certainty is not always available. The decision framework above can help you identify which comments are clear enough to assume.

The Silent Assumption Pattern

This pattern occurs when the author makes a change but does not explain it in the response letter. The reviewer sees the change but does not understand why it was made. The reviewer may think the author ignored the comment or made an arbitrary change.

The cause is a failure to document the reasoning. The response letter is the place to explain your interpretation. Without that explanation, the reviewer cannot evaluate whether your change addresses their concern.

The Escalation Failure Pattern

This pattern occurs when the author encounters a genuinely ambiguous comment but does not ask the editor. The author makes a guess, the guess is wrong, and the revision fails. The author could have avoided the problem by asking a question early in the process.

The cause is a reluctance to escalate. The author may not want to bother the editor or may not know that asking is acceptable. The Committee on Publication Ethics Core Practices support a transparent peer review process, and asking the editor for clarification is a legitimate part of that process.

Welfare and Safety Context

The Human Element of Peer Review

Peer review is a human process. Reviewers are volunteers who spend time reading your manuscript and writing comments. They may be tired, busy, or working under their own deadlines. Their comments may be rushed or imprecise. This does not mean the comments are invalid, but it does mean you should interpret them with some tolerance.

The same applies to you as the author. You may be under pressure to publish, to meet a grant deadline, or to complete a degree. The revision process can be stressful. The decision framework is designed to reduce that stress by giving you a clear path forward.

The Integrity of the Record

The publication record is the foundation of scientific communication. When you respond to reviewers, you are helping to ensure that the record is accurate and transparent. The National Library of Medicine's research methods resources emphasize the importance of rigorous methodology and transparent reporting. Your response to reviewers should reflect those values.

If you are uncertain about a comment, the uncertainty is not a sign of failure. It is a sign that the comment needs more thought. The decision framework helps you think through the comment systematically.

The Role of Reporting Guidelines

Reporting guidelines are checklists that help authors report their research completely and transparently. The EQUATOR Network maintains a library of reporting guidelines for different study types. If a reviewer asks you to follow a reporting guideline, the request is usually specific and actionable. You can find the appropriate guideline on the EQUATOR Network and use it to structure your revision.

If a reviewer asks you to report something that is not in the guideline, you may need to ask for clarification. The guideline is a baseline, not a ceiling. The reviewer may be asking for something that is specific to your study.

Limitations and Boundaries

What the Decision Framework Cannot Do

The decision framework cannot tell you what a specific reviewer meant by a specific comment. It can only help you assess the comment's specificity, the risk of misinterpretation, and the timeline. The final judgment is yours.

The framework also cannot resolve conflicts between reviewers. If two reviewers ask for contradictory changes, you need the editor to decide. The framework can help you identify the conflict, but it cannot resolve it.

Jurisdiction and Policy Boundaries

The framework is based on general publication ethics and research methodology standards. It does not replace the specific instructions of a journal or the policies of a funding agency. The National Institutes of Health has specific policies for grant applications and award management. If your manuscript is part of a funded project, you should check the funding agency's requirements for publication and data sharing.

The NIH Data Management and Sharing Policy describes expectations for data management and sharing. If a reviewer asks about data availability, the request is likely to be clear and actionable. You should check the policy to ensure your response is consistent with the funding agency's requirements.

The Limits of the Sources

The sources cited in this article provide general guidance on publication ethics, research methods, and reporting standards. They do not provide a specific protocol for responding to reviewer comments. The decision framework is a synthesis of practical guidance from these sources, not a rulebook.

Professional Escalation Criteria

When to Ask the Editor

You should ask the editor when the comment is genuinely ambiguous and the risk of misinterpretation is high. You should also ask when two reviewers give contradictory comments. The editor is the person who can resolve these issues.

You should not ask the editor when the comment is clear. Asking in that situation wastes the editor's time and may create a negative impression.

When to Escalate Beyond the Editor

If the editor does not respond to your question, or if the editor's response is not helpful, you may need to escalate. The escalation path depends on the journal. Some journals have a managing editor or a publisher who can help. The Committee on Publication Ethics Core Practices describe the responsibilities of journals and publishers in handling disputes.

If you believe the peer review process has been unfair or unethical, you may need to contact the journal's publisher or the Committee on Publication Ethics. This is a serious step and should be taken only when you have documented evidence of a problem.

When to Withdraw the Manuscript

Withdrawal is a last resort. If the reviewer's comments are impossible to address without compromising the integrity of the study, and the editor does not provide a reasonable path forward, you may need to withdraw the manuscript and submit it elsewhere. This is a difficult decision, and you should seek advice from a mentor or a colleague before making it.

Frequently Asked Questions

What is the difference between assuming and asking in a reviewer response?

Assuming means you make a reasonable interpretation of the comment and implement the change. Asking means you contact the editor for clarification before making the change. The decision depends on the comment's specificity, the risk of misinterpretation, and the revision timeline.

How do I know if a reviewer comment is specific enough to assume?

A comment is specific enough to assume when it names a section, a variable, a method, or a figure. If the comment describes a general problem without pointing to a location or a fix, you should consider asking for clarification.

What should I do if two reviewers give contradictory comments?

You should ask the editor. The editor is the person who can resolve the conflict. You should not try to satisfy both reviewers if the requests are mutually exclusive.

Can I ask the reviewer directly for clarification?

No. The standard process is to ask the editor, who will relay the question to the reviewer. Asking the reviewer directly bypasses the journal's process and may not be allowed.

How long should I wait for the editor's response before proceeding?

The journal's instructions may indicate a response time. If the journal does not specify, a reasonable wait is one to two weeks. If you do not receive a response, you can follow up with the editor.

What should I include in my response letter?

Your response letter should include every comment and your response to it. State whether you made a change, what the change was, and where it appears in the manuscript. If you asked a question, state the question and why you asked it.

What if I cannot implement the reviewer's request?

If you cannot implement the request, you should explain why in the response letter. You may need to ask the editor for guidance if the request is central to the study's validity.

How do I handle a reviewer comment that is not about my study?

If a reviewer comment is not relevant to your study, you can explain why the comment does not apply. You should be respectful and provide a clear rationale. If the comment is a misunderstanding, you can clarify the misunderstanding in the response letter.

Using the Evidence

Related Articles

• Observational vs. Experimental Studies: A Decision Framework for Life Science Researchers
• Careers in Agriculture: A Decision Framework for Choosing Your Path
• T-Test vs ANOVA: A Decision Framework for Comparing Group Means
• PCR Troubleshooting: A Decision Framework for Weak, Missing, or Nonspecific Bands
• Choosing a Bioinformatics Master's Program: A Decision Framework

References and Further Reading

• Research Methods Resources. National Library of Medicine.
• EQUATOR Network. EQUATOR Network.
• Core Practices. Committee on Publication Ethics.
• NIH Grants and Funding. National Institutes of Health.
• ORCID for Researchers. ORCID.
• Data Management and Sharing Policy. National Institutes of Health.
• NCBI Literature Resources. National Center for Biotechnology Information.
• PubMed. National Library of Medicine.

This article is educational and does not replace institutional policy, professional advice, or applicable safety and regulatory requirements.