PMean: Writing the methods section of a research paper

Steve Simon


I’m teaching a class on Clinical Research Methodology and at least a few of the students are confused about what to put in the methods section of a research paper or a thesis. They’re confused? I’m even more confused than they are. Every paper and every thesis is different, so it is impossible to offer any coherent guidance. But let me try anyway.

It helps to see the variety of different formats that are presented in various research papers and web sites. There is no consistency and often very little in common. Here are some examples.

Alice Frye’s Powerpoint presentation also see this presentation and this one as well) lays out the methods section requirements with great detail.

Richard Kallet has a nice publication in Respiratory Care.

Elena Kallestinova’s publication in the Yale Journal of Biology and Medicine provides a structure through a series of questions.

The International Committee of Medical Journal Editors have published a general guide to writing a paper with a fair amount of detail about what goes in the methods section.

Asghar Ghasemi and others have a nice publication in the International Journal of Endocrinology and Metabolism with only two major sections (but several subsections in each).

Are you confused yet? Don’t despair. The fact that there are so many different standards out there means that you have a lot of latitude in how to structure your methods section. The best advice I can offer is to read a half dozen articles or theses and take notes about what these writers did.

Let me offer my own suggestion for what goes in a methods section. It is a synthesis of all of the above plus some additional resources.

First of all, keep in mind the two reasons that you are writing a methods section. First, you are providing enough information that a reasonably intelligent person could repeat your research study using roughly the same approach that you did. It does not have to document every last detail. Don’t bother describing things that are routine and well understood by everyone in your field. Second, you are helping anyone who is reading your research to assess the quality of your work.

An important dividing line comes between the methods section and the results section. You can present some data in the methods section, but only that information that was available before you started your study. Anything after that belongs in the results section.

Your methods section should have five sections:

If you don’t have anything for a particular section, it’s okay to drop it. If you have a different section that you want to add, that’s fine also. Use this (or any of the guides mentioned above) as a framework, but adapt it to the needs of your particular research. Let’s talk about each of these sections in a bit more detail.

Participants. Tell where you plan to find your participants. Describe any monetary incentives for participation. List the criteria that you will apply to decide who to include and who to exclude. Document any special efforts that you take to insure representativeness.

Materials. If you use any exotic supplies or chemicals, describe them here. List the company where you procured them if they are not commonly available.

Procedures. You only need to document the non-routine procedures. This might involve the details on running complex equipment or the steps in a laboratory method. If these procedures are described in a peer-reviewed publication, you might want to include that reference here.

Measures. Describe the variables that you will measure. Not every single measurement, but just those that are important. These would include your outcome variables, your independent variables, and key covariates. You should present information about the validity/reliability of any variable that warrants it. This is a judgement call, of course.

Analysis. Describe how you plan to analyze your data. Most analyses start with some simple descriptive statistics: means and standard deviations for continuous variables and percentages for categorical variables.

Provide your research hypothesis in this section, and state whether it is one-sided or two-sided. One-sided hypotheses require a brief justification, along with an assurance that the direction of the hypothesis was selected prior to data collection. Mention the statistical test that you plan to use. If you are running more than one test, explain what measures you will use to control the Type I error rate. In some settings, it may be acceptable to not make adjustments for multiple tests, but you should state this explicitly.

You do not need to provide references for simple and commonly used statistics, like a t-test, linear or logistic regression, or analysis of variance. More complex procedures should include a reference. If you are referencing a book, remember that a page or page ranges are needed.

You need to define how you will handle missing values and dropouts. If you plan to exclude extreme values (outliers) from your data set, give an objective rule here.

Specify what statistical software you plan to use for your analysis (e.g., SPSS, SAS, or R) and be sure to include the version number. State any special libraries or macros that you used within your statistical software system. If your software is relatively uncommon, be sure to include a reference that explains how the software works and where you can obtain it.

Somewhere in this outline (probably in the analysis section), you need to explain about the ethical review (if any) that your research received. If your research is exempt from review, state this clearly.

You also need to justify your sample size, and this usually fits best in the analysis section. If the goals of your research are qualitative, then the sample size justification can also be qualitative.

Final thoughts. This outline might be a good starting point for many research studies, but it might not be right for you. Don’t force your methods section into this organizational style. Every research study is different.

I have a web page about writing a methods section for a research grant that you might also find helpful.