Your Reviewer Says “The Methods Are Not Clear.” What Do They Actually Want?
When a reviewer says “the methods are not clear,” they usually need enough information to understand who was studied, how participants or data were selected, what was measured, what happened during data collection, how the analysis was conducted and why the methods fit the research question. Do not respond by making the section longer everywhere. Diagnose the specific missing link.
“Please clarify your methods.”
Four words.
Twenty-seven possible problems.
The worst response is:
Add three pages everywhere.
Clarity is not the same as length.
First identify what the reader could not reconstruct.
Diagnostic 1: who exactly was studied?
The Methods section says:
“Participants were women of reproductive age.”
The reviewer may still need:
- age definition;
- residence requirements;
- inclusion criteria;
- exclusions;
- whether pregnant women were included;
- where participants were recruited;
- study period.
A population label is not an eligibility procedure.
Weak:
Women aged 15-49 were included.
Better:
Eligible participants were women aged 15-49 years who had resided in the study area for at least six months and attended one of the selected facilities during the data-collection period. Women unable to provide informed consent were excluded.
Only include criteria you actually used.
Diagnostic 2: how were they selected?
“Random sampling” is not enough.
A reviewer may be asking:
- What was the sampling frame?
- What was randomized?
- At what level?
- How were replacements handled?
- Was sampling clustered?
- How were qualitative participants purposively selected?
- How many declined?
Weak:
Participants were randomly selected.
Stronger:
A numbered list of 1,200 eligible nurses was obtained from facility HR records. Two hundred unique IDs were selected using a computer-generated simple random sample without replacement.
Now another researcher can understand the procedure.
Diagnostic 3: what exactly was measured?
Methods often use constructs without operational definitions.
Examples:
- quality of care;
- adherence;
- depression;
- access;
- knowledge;
- empowerment;
- satisfaction.
The reviewer may need:
- instrument;
- items;
- scoring;
- cut-off;
- recall period;
- validity;
- adaptations;
- translation;
- outcome definition.
Weak:
Depression was assessed using PHQ-9.
Stronger:
Depressive symptoms were measured using the nine-item PHQ-9, with items referring to the previous two weeks. Scores were summed to [range]; the primary analysis used [continuous score/cut-off], as prespecified.
Use the actual scoring and validation approach.
Diagnostic 4: what happened to participants or data?
A Methods section can list instruments without describing procedure.
The reviewer may need:
- where interviews occurred;
- who administered them;
- interviewer training;
- duration;
- privacy;
- follow-up timing;
- intervention exposure;
- specimen handling;
- record abstraction;
- quality assurance.
For qualitative studies:
“Interviews were conducted.”
is rarely enough.
Describe:
- interviewer role/background where relevant;
- interview setting;
- guide development;
- language;
- recording;
- transcription;
- field notes;
- repeat interviews where applicable.
COREQ can help identify reporting omissions for interview and focus-group studies.
Diagnostic 5: how were the data analysed?
Weak quantitative Methods:
Data were analysed using SPSS. Chi-square and logistic regression were performed.
The reviewer still needs:
- outcome definition;
- effect measure;
- objective-test link;
- covariate selection;
- missing data;
- clustering;
- weighting;
- significance/CI approach;
- model assumptions;
- interaction/effect modification;
- software version where relevant.
Weak qualitative Methods:
Thematic analysis was performed.
Which version?
How?
Who coded?
Inductive/deductive?
Codebook?
Reflexive process?
How were themes developed?
Was analysis concurrent with data collection?
What role did the conceptual framework play?
The method label is not the method.
“We used regression” and “we used thematic analysis” are analysis names, not reproducible analysis descriptions.
Diagnostic 6: why were these methods appropriate?
Sometimes the procedures are clear.
The logic is not.
Reviewer:
“Why was a cross-sectional design used?”
Weak response:
“Because it is cost-effective and takes less time.”
That explains feasibility.
Not fit.
Better:
“A cross-sectional design was selected because the primary objective was to estimate current prevalence and examine associations among variables measured during the same study period. The study was not designed to establish temporal or causal effects.”
Now the design is connected to the question.
responding to a reviewer
Reviewer comment:
“Please clarify how participants were selected and how sample size was determined.”
Bad response:
“Thank you. We have clarified the Methods.”
Better response:
“Thank you. We revised the Sampling subsection to specify the facility sampling frame, the two-stage selection procedure and handling of non-response (page 7, lines 142-158). We also expanded the sample-size paragraph to state the primary parameter, assumed prevalence, confidence level, precision, design effect and non-response allowance (page 8, lines 159-171).”
Then make the manuscript changes.
The response letter should tell the reviewer exactly where the problem was repaired.
Do not hide behind “as previously described”
Sometimes space is limited.
But:
“Data collection was conducted as previously described [12].”
can force readers to retrieve another paper to understand essential methods.
Use citations for established protocols.
Still include enough information for the current study to be interpretable.
Especially if:
- procedures changed;
- population differs;
- timing differs;
- outcomes differ;
- analysis differs.
Use reporting guidelines as a diagnostic tool
Before resubmission, find the guideline for your design.
Examples:
- CONSORT → randomized trials;
- STROBE → observational studies;
- COREQ → qualitative interviews/focus groups;
- PRISMA → systematic reviews;
- CHEERS → health economic evaluations.
A checklist does not guarantee methodological quality.
It can reveal reporting gaps.
That is precisely useful when someone says:
“Methods unclear.”
What do I actually write in a Methods clarity audit?
Use six headings:
WHO?
Population, setting, eligibility, recruitment.
HOW SELECTED?
Sampling frame, sampling method, response.
WHAT MEASURED?
Variables, instruments, definitions.
WHAT HAPPENED?
Data-collection/intervention procedure.
HOW ANALYSED?
Analytic method, assumptions, missing data, design features.
WHY THIS METHOD?
Alignment with research question.
If a reviewer could not answer one of those after reading the Methods, that is likely the problem.
Bench Check: clarity theatre
You add:
“The study adopted a rigorous descriptive quantitative cross-sectional research design using a systematic methodological approach to collect robust empirical data.”
Longer.
Still unclear.
Prefer:
“We conducted a cross-sectional survey because the primary objective was to estimate current contraceptive use and examine associations with participant characteristics.”
Scientific writing becomes clearer when abstract praise is replaced by procedure.
Give your Methods section to someone who did not work on the study.
Ask them to answer:
- Who was eligible?
- How were they selected?
- What was the primary outcome?
- How was it measured?
- What happened during data collection?
- What analysis answered the main objective?
Do not explain verbally.
Every unanswered question is an edit.
Frequently asked questions
- How long should a Methods section be?
Long enough to understand and appraise what was done. Journal limits vary, but clarity and reproducibility matter more than arbitrary length.
- Should I include sample-size calculations?
Usually, explain how the sample size was determined for designs where a formal calculation or justification is relevant.
- How much detail about statistical analysis is enough?
Enough to understand what was estimated, which model/test was used, how covariates and design features were handled and how uncertainty was quantified.
- Do I need to describe standard instruments?
Yes, at least enough to identify the instrument, scoring/use in your study and relevant adaptation/validation. A citation can provide additional detail.
- How do I respond to “methods unclear” if the reviewer is vague?
Diagnose the six domains above, revise the likely gaps and state exactly what was changed in the response letter.
Use the Methods Bench Methods Clarity Audit:
Who → selection → measurement → procedure → analysis → justification
References and further reading
- 1.ICMJE Recommendations. Preparing a Manuscript for Submission to a Medical Journal.
- 2.EQUATOR Network reporting-guideline library.
- 3.STROBE Statement.
- 4.CONSORT Statement.
- 5.COREQ guideline.
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