How to Write a Methods Section of a Research Manuscript: 

Avoiding 6 Common Mistakes

The Methods Section usually is considered an easy section to write.  However, mistakes abound.  Articles on How to write a methods section usually provide rules.  Instead, here are tips to avoid 6 common mistakes.

1.    The description of each method is written in present or future tense.  The Methods section of a clinical or scientific manuscript (or clinical study report) should describe what procedures or techniques were actually done.   Thus, the methods section should be written in past tense.  In contrast, a procedure describes what should be done and is written in either present tense with action verbs or in future tense. 

2.    Common methods are described in great detail.  If the technique has been described previously and authors use a few modifications, then the authors should cite a reference for the procedure and state something like “as previously described (reference) with the following modifications.”   Common modifications are the primary antibodies for immunohistochemistry or western blot.   

3.    Sufficient details are not provided for a scientist skilled in the art to be able to reproduce the technique.  For example, western blotting is a relatively common technique.  The specificity of the assay is dependent on the specificity of the primary antibody for each protein:  thus, the method for Western blot should include  the target protein of the antibody, the antibody’s type (polyclonal antibody or monoclonal isotype), concentration (if different than manufacturer’s recommendation), and its source (Manufacturer, City, State or Country).  As a second example, protein lysate fractions separated during ultracentrifugation in swinging buckets vs fixed buckets can differ at the same g-force. Thus, the methods should provide the rotor and g-force. As a third example, immunohistochemistry for some antigens requires pretreatment with specific chemicals or enzymes (often called antigen retrieval). Authors should mention these conditions for exposing the antigen. 

4.    The described statistics are not adequate for full analysis of the experiments.  The statistics section should fully describe the analyses used to determine significance for the continuous variables and parametric variables.  For example, the manuscript did not mention any power calculations that determined the appropriate size of the groups that were compared.  As a second example, if associations were examined between many variables on the same data, then authors and statisticians should consider whether use of the Bonferroni correction is appropriate.  

5.    Results are intermixed with the Methods. In most cases, the results should be placed in the Results section.  In some journals, the explanation between the number of patients screened for enrollment and the number of enrolled patients is kept in the Methods section. In other journals, the difference between screened and enrolled patients is explained in the first paragraph of the results section. 

6.    Guidelines for reporting the specific method or type of clinical trial were not followed or the descriptions were not complete.  For example, reporting of specific laboratory procedures such as T cell assays need to include well defined details that are stated in the MIATA guidelines where MIATA stands for Minimal Information About T cell Assays. Its guidelines are listed at .  The reporting guidelines for different types of clinical trials are listed by the . Guidelines for reporting animal studies are listed at ARRIVE.

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