How to write the Methods section of a research paper

The Methods section of a research article is like a roadmap leading to the core of the research, guiding the readers through the actual journey the authors took to reach their destination. In the manuscript, this section contains the essential details for other scientists to replicate the experiments of the study and help the common readers to understand the study better.

The descriptive nature of this section may make it seem one of the easiest parts of a manuscript to write. However, this is also the part, where the details are often missed while writing, and sometimes during reading due to its highly technical nature’.

In this article, we will share some tips to make the Methods section of your manuscript interesting and informative. While the article uses examples mostly from the biomedical and clinical research studies, authors from other fields too would find the tips useful for preparing their next manuscript.

Break ice between the readers and the Methods section

First, let’s ponder over the issue of the perception of boredom we often associate with the Methods section of an article. It may be the names of the reagents and instruments, separated by some numbers in terms of some concentrations or the technical terminologies that make the reading a heavy-duty task. Listed below are some useful ways of breaking the ice between the Methods section and the readers:

1. Explanation: Usually, each paragraph or subsection of the Methods section talks about a specific experiment. Early in each paragraph, explain the rationale behind your choices of that particular experiment.; for example, why you used a certain compound, a specific strain of mice as the experimental model or the particular concentration of that key reagent.

For clinical research, providing a detailed rationale for selecting the exclusion or inclusion criteria can be a good idea to present early in the Methods section. If you took a conventional or widely used method, you certainly don’t need to appear stating the obvious, but for less conventional approaches sharing your reasoning of the study design instantly makes the readers curious and engaged with your paper.

2. Visual presentation: To help the readers follow the study design or methodology better, visual elements like the schematic diagram, flowchart, and table can be used in this section. They help in breaking the monotony and making the absorption of complex information easy.  

The dos and don’ts of writing the Methods section

Secondly, the information in the methods section is closely scrutinized by the journal editors and peer reviewers to assess whether the most appropriate technique was used to reach your research goal. While every detail of your experiment need not be included, the essential and critical steps should be well described to receive a positive peer review.

The essential do’s and don’ts of writing a technically sound Methods section:

Do’s

1. Adhere to the specific guidelines: Read the author’s instruction section of your target journal carefully and follow the specific instructions. For example, the heading of the section “Materials and Methods” may need to be changed to “Patients and the Method” to follow the guidelines of your target journal or the name of the institutes could be omitted for the journals that do not prefer open-label reporting. Also, you may be expected to follow a particular style guideline like the one published by the American Psychological Association while writing the Methods section.

Biomedical researchers would benefit from using the checklists for different study types to ensure the essential details are included in the Methods. Some of the standardized and widely referred checklists include the ones for randomized clinical trials CONSORT (Consolidated Standards of Reporting Trials), cohort, case-control, cross‐sectional studies STROBE (STrengthening the Reporting of OBservational studies in Epidemiology), diagnostic accuracy STARD (STAndards for the Reporting of Diagnostic accuracy studies), systematic reviews and meta‐analyses PRISMA (Preferred Reporting Items for Systematic reviews and Meta‐Analyses), and Case reports CARE (CAse REport).

2. Structure the section so that it tells the story of your research: All the experiments should be presented in a logical manner that helps the reader retrace the gradual and development and nuances of the study. A useful way of achieving this is to describe the methods in a chronological order of the experiments. For example: for a clinical trial, you may start with the setting and time of the study (the beginning and termination dates of the study), followed by the details of the patient recruitment (Number of subjects/patients etc.), study design (prospective, retrospective or other), randomization (if any), assigning into groups, intervention, and describing the techniques used to collect, measure, and analyse data.  

3. Follow the order of the results: To improve the readability and flow of your manuscript, match the order of specific methods to the order of the results that were achieved using those methods.

4. Use subheadings: Dividing the Methods section in terms of the experiments helps the reader to follow the section better. You may write the specific objective of each experiment as a subheading. Alternatively, if applicable, the name of each experiment can also be used as subheading.

5. Provide all details meticulously: Provide the details that you considered while designing the study or collecting the data because the smallest variations in these steps may affect the results and interpretation of their significance. When employing the outcome measures, the readers would like to know the information regarding validity and reliability. The correct way of reporting the reliability and the validity depends on the specific research design. Usually, information from existing literature is presented to support for the reliability and the validity of a measure.

Carefully describe the materials, equipment (like testing instruments and technical equipment), or stimuli used in the experiment. If your study involved a survey or any psychological assessment, mention the questionnaire, scoring methods, and validation of scales with every possible detail.

Also, be careful about one common manuscript error i.e. not mentioning the sample size estimation (whenever relevant). Although the estimated sample size is computed before the actual study starts, it helps the reader assess the expected change in the outcome variables and the number of subjects needed to detect that change within a certain confidence range. Similarly, mentioning power calculation is a critical point to be mentioned in the Methods section.

6. Mention the ethical approval: If relevant, early in the Methods section mention whether your study was approved by the ethics committee or institutional review board, and whether you have received oral/ written informed consent from the patients or the guardians.

7. Specify the variables: Clearly mention not only the control variables, independent variables, dependent variables but also if there were any extraneous variables that might influence the result of your study. For example, in a tutorial on learning how to write ‘Research Methodology’, one group is provided with a traditional text while the other group is provided with an interactive online tool. However, if some participants already have prior knowledge of ‘how to write the Methods section’, this pre-knowledge will act as an extraneous variable.

8. Statistical analysis:  In this section, describe all statistical tests, levels of significance, and software packages used to conduct the statistical analysis. You may also consult the biostatistician of your team to receive help to write this section. Don’t forget to indicate if the recommendations of a knowledgeable and experienced statistician were considered. Finally, it is important to provide the justification of the preferred statistical method used in the study. For example, why the author is using a one-tailed or two-tailed analysis.

Don’ts

1. Do not describe well-known methods in detail: For the sake of brevity, avoid listing the details of the experiments that are widely used or already published in numerous articles in your field of research. Instead, mention and cite the specific experiment and mention that the referred process was followed. However, if you have modified the standard process to meet the specific aim of your study, do describe the modifications and the reasons for those in sufficient detail.

2. Do not provide unnecessary details: Avoid unnecessary details that are not relevant to the result of the experiment. For example, you need not mention trivial details such as the color of the bucket that held the ice. Try to stick only to the details that are relevant and have an impact on your study.

3. Do not discuss the pros and cons of other methods: While it may be tempting to discuss the reasons why you did not use a particular method or how your chosen method is superior to others, save these details for the Discussion section. Utilize the Methods section only to mention the details of the methods you chose.

To summarize all the tips stated above, the Methods section of an ideal manuscript aims to share the scientific knowledge with transparency and also establishes the robustness of the study. I hope that this article helps you to reach the goal of writing a perfect manuscript!

Suggested reading:

• Manuscript structure: How to convey your most important ideas through your paper
• The secret to writing the introduction and methods section of a manuscript
• Supply adequate details of items mentioned in the materials and methods section