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What to include in the Methods section of a research paper

The Methods section of your research paper explains how you did the study. This information allows your reader to judge the validity of your findings and repeat or adapt your experiments if they wish. To help your reader find the information they need, the Methods section needs to be clearly structured and contain the relevant details. In this blog post, I explain how to structure the Methods section so the methodological information is easily accessible.

What to include

The Methods section should include the following information:

  • The study design
  • What you studied (animal model, human participants, cells, etc.)
  • What you used (equipment and materials with manufacturer’s details)
  • What you measured (outcome measures)
  • How you collected your data
  • How you analyzed your data.

Your reader will find what they are looking for more easily if you put this information into subsections with subheadings. Starting with a description of the study design makes sense because the Introduction section typically ends with a brief description of the experimental approach. And ending with a description of how the data were analyzed provides a nice transition to the Results section.

 

Check the author guidelines of your chosen journal for specific instructions on how to structure your Methods section. Some journals ask their authors to follow reporting guidelines. These guidelines are specific to the study type and they improve the quality of your article by ensuring that all the relevant information has been included.

Now let’s take a closer look at what should be included in each subsection.

Study design

Start by briefly describing your study design. For a clinical trial, give the type of trial (e.g., parallel, crossover, factorial) and hypothesis (i.e., specify whether you are looking for superiority, non-inferiority, or equivalence). If you are testing a new drug, specify the phase of your trial (i.e., I–IV). For animal research, describe the groups that are being compared (e.g., wild-type mice versus genetically modified mice). If no control group has been included, explain why. For example, you may not need a no-treatment control group if you are comparing oral versus intraperitoneal injection of a drug. Promote research integrity by stating which groups were used in each experiment. This shows your reader that you haven’t deliberately excluded any groups because of unexpected results.

Your reader will want to judge whether bias could have affected your results. Describe how you randomized animals or human participants to each group, and whether researchers were blinded to the group allocation throughout the study. This will help your reader to judge whether the reported outcome effects have been overestimated.

What you studied

Animals

In animal studies, give the species, strain, sex, weight, and age of the animals if feasible. Specify when you measured the body weight (e.g., at baseline) as this may vary during the course of the study. For most species, it is more informative to give the age in weeks rather than referring to a developmental stage. For example, mice reach sexual maturity at around 5 weeks of age and start to be affected by senescence at around 6 months. This is a broad age spectrum, so referring to ‘adult’ mice in your paper will not help your reader.

Human participants

In trials with human participants, clearly describe the eligibility criteria you used to select your participants. This will tell your reader which populations your results apply to and how relevant your findings are to their own clinical practice. Report how you recruited your participants and whether you obtained their informed consent. If the need for informed consent was waived, say so and explain why.

Ethical approval

Studies involving animals and human participants usually require ethical approval. State who granted ethical approval for your study and give the approval number.

Sample size

Tell your reader how you calculated your sample size. Describe the power calculation you used and the primary outcome this calculation was based on. This information is important because it indicates the probability that your study will find a clinically or scientifically important difference. In animal studies, it also shows that you haven’t used more animals than necessary. Give the number of animals you included in each group and each experiment. This will help the reader to assess the validity of your results.

Study setting

Tell your reader where your data were collected. In a clinical trial, describe the setting in which your participants were studied, giving the type of clinic, specific location, and name of the institution. These details will help your reader to decide whether your findings are applicable to their own clinical setting. In animal studies, describe where the experiments were performed (e.g., in the laboratory, animal facility, open field, home cage, etc.), including any periods of acclimatisation. If multiple sites were involved, specify where each experiment was performed.

Interventions or experimental procedures

In a clinical trial, describe the interventions you studied for each group, including any control interventions. Your reader should be able to repeat the interventions you describe in their own clinical setting. For example, if you administered drugs to your participants, give your reader the name and dose of the drug and tell them how and when it was administered. Give the exact dates the study was conducted and specify the disease or condition that was studied and how it was defined.

In studies using animal models, explain how you developed your specific model (e.g., drug treatment, surgical procedures, or pathogen infection), the methods you used to measure the outcomes (e.g., behavioural testing or measuring biological parameters in the animals), and relevant post-experimental procedures (e.g., euthanasia and tissue collection). Also, give details about animal care and handling because these can affect the results.

Give complete details of all the equipment and materials you used in your study, including the manufacturer’s details. Give the research resource identifier (RRID) if possible. These are more helpful than catalogue numbers because they are unique to a particular product and they do not change; the catalogue number you give for a particular antibody may not be valid in 3 years, leaving your reader with no way to find it. Visit the RRID website for a comprehensive list of RRIDs for common research resources.

Outcome measures

An outcome measure is a variable that measures the effects of a specific intervention. Studies often have several outcome measures, which are categorized as primary or secondary outcomes. The primary outcome is the most important and is used to calculate the sample size. Secondary outcomes are less important but are still relevant to evaluating the effect of the intervention. Clearly define your primary and secondary outcomes, giving details on how and when they were evaluated. You should provide enough information to allow your reader to study the same outcomes in their own clinical/experimental setting.

Tell your reader exactly what was measured. For example, in a study on spatial learning, one outcome measure may be the ability of mice to find the submerged platform in the Morris water maze test. Did you measure how long it took the mouse to find the submerged platform or how far the mouse travelled before finding the platform?

Statistical analysis

Describe the statistical methods you used for each experiment so the reader can evaluate the appropriateness of the analysis and whether the conclusions are valid. Include the outcome measures, independent variables, and which tests you used. Explain how you handled any missing data and how you adjusted for multiple comparisons. And say which software you used for the analysis.

Don't forget the details

The purpose of the Methods section is to give your reader enough information to repeat your experiments and interventions. Don’t skip important details to meet your journal’s word limit. Instead, put additional information into the supplementary information, or refer your reader to a previous publication that describes the method in full. But make sure the citation is precise and accurate. A common mistake is referring the reader to a publication that then refers them to another publication. The methodological information must be easily accessible.

Research integrity

The Methods is an important section of your research paper because it allows your reader to repeat your experiments and validate your findings. This is critical for transparency and integrity in scientific research. Following the tips outlined in this post and in the various reporting guidelines will help you to write a clear and informative Methods section that increases the quality of your research paper.

With the proper instructions, your reader can validate your findings

Claire Bacon is a former research scientist with professional qualifications in copy editing and medical editing. She edits manuscripts for non-native English-speaking scientists and works as a copy editor for a medical journal.

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