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Research Design and Methods. Betsy Myers Hospital for Special Surgery. Research Plan. Portray What you intend to do Specific Aims Why it is important Background and Significance. Research Plan. What has been done so far Preliminary Studies How you are going to do it

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Research Design and Methods

Betsy Myers

Hospital for Special Surgery

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Research Plan


  • What you intend to do

    • Specific Aims

  • Why it is important

    • Background and Significance

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Research Plan

  • What has been done so far

    • Preliminary Studies

  • How you are going to do it

    • Research Design and Methods

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Getting Started

Read instructions on how to prepare Research Design and Methods section

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“Describe the research design conceptual or clinical framework, procedures, and analyses to be used to accomplish the specific aims of the project.”

Instructions for PHS 398 Rev. 09/2004

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“include how the data will be collected, analyzed, and interpreted as well as the data-sharing plan as appropriate.”

Instructions for PHS 398 Rev. 09/2004

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“Describe any new methodology and its advantage over existing methodologies. Describe any novel concepts, approaches, tools, or technologies for the proposed studies.”

Instructions for PHS 398 Rev. 09/2004

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“Discuss the potential difficulties and limitations of the proposed procedures and alternative approaches to achieve the aims.”

“provide a tentative sequence or timetable for the project.”

Instructions for PHS 398 Rev. 09/2004

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Main Points That You Must Get Across

  • Research design, if carried out successfully, will accomplish Specific Aims

  • Methods are feasible and well developed

  • Approach is original

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Main Points That You Must Get Across

  • Data will be analyzed correctly

  • Enough subjects/specimens will be tested to lead to conclusive results

  • Limitations are of minor concern only

  • Study can be accomplished in requested time

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  • No one organization fits all proposals

  • Try to organize in logical sequence of Specific Aims and corresponding experiments

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Start with an outline


  • D1. Overview

    • Flowchart

    • Brief description

  • D2. Aim 1

    • Rationale

    • Design

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  • Write for reviewers and funding agency staff

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  • Reviewers are informed readers but not necessarily experts in your specific area

  • Funding agency (NIH) personnel want to know health impact

  • Keep in mind that you need to be very clear and you need to emphasize health significance throughout

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Consider giving overview at start of entire section

  • Describe overall approach that will be used to achieve aims

  • Consider using flowchart or table

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Example of Chart

Aim 2

Aim 1


Ex-vivo analysis










Part 2

Part 1

Aim 3



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For Each Specific Aim

  • Reiteration of Research Question

  • Rationale

  • Design, Approach

  • Methods

  • Anticipated Results, Interpretation

  • Difficulties, Limitations, Alternative approaches

Or could include section on

Detailed Methods

common to more than

one Specific Aim

after description of Aims

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  • Directly and succinctly reiterate why you are doing this Specific Aim

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Briefly describe

  • Design of study

  • Choice of specimens

  • Choice of interventions/independent factors and outcome assessments

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Describe techniques and equipment for measuring all variables

  • Use illustrations

  • Demonstrate that measurements will be accurate, precise, sensitive, specific

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Novel Methods

  • Emphasize what is new about your methods

  • Point out advantages to using your proposed techniques over other approaches

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Data Analysis

Describe approach for data analysis in detail

Conclusions &


Raw Data

Analysis should not

be Black Box

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Data Analysis

If using analytic statistics, specify

  • Statistical parameters and tests

  • Assumptions of tests

  • Alpha level

    • Alpha = probability of falsely rejecting null hypothesis

  • Reference if statistical approach is not well known

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Power Analysis

  • Remember that you need to determine

    • How many specimens are needed to have a certain probability of detecting an effect?

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Keep in Mind...

  • Goal is to demonstrate that enough data will be collected to support analysis

  • Straightforward procedure

  • But is “ballpark” approach

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Number of Specimens in Research Plan

State assumptions and methods used for power analysis

  • Specify primary outcome variable

  • Specify factor(s) or independent variable(s) of interest

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Number of Specimens in Research Plan

  • State proposed statistical test or interval estimation


    • Analysis of variance

    • Linear regression

  • Note that each test has specific formula for power/number of specimens

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Number of Specimens in Research Plan

  • Give alpha level

    • Alpha = probability of falsely rejecting null hypothesis

  • Give beta level or power

    • Beta = probability of falsely accepting null hypothesis

  • Describe effect size

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Effect Size

“…to answer the question ‘What are my chances of finding it?’, the researcher needs to have some idea of how big ‘it’ is”

J Cohen

Statistical Power Analysis for the Behavioral Sciences

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Effect Size

  • Ratio of expected difference to measure of variability

  • Based on

    • Published work

    • Preliminary studies

    • Educated guess

      Use an effect size of scientific or clinical importance

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Number of Specimens

  • Calculate number

    • Hand calculation

    • Computer programs, e.g., nQuery, PASS

  • If using educated guess for effect size, determine number for several effect sizes

  • Adjust for loss of laboratory animals if applicable

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Expected Results and Interpretation

Remember to discuss expected results and interpretation of analysis






Interpretation of

results to answer...



Analysis of


Collection of


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  • Include segment on potential difficulties & limitations at one of following locations

    • Under each Specific Aim

    • End of entire Research Design and Methods section

    • As they occur in methods

  • Use limitations to point to future studies

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Include timeline or timetable at end of Research Design and Methods

  • Give enough detail for evaluation

  • Make certain it is reasonable

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  • Close Research Design and Methods with overall statement about significance of studies

  • Be enthusiastic

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Tips on Clarity and Style

Make appearance conducive to easy reading on paper and on screen

  • Neat

  • White space

  • 11-12 point font

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Tips on Clarity and Style

  • Proofread

  • Make figures, tables, and legends legible

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Stick to page length recommendations

  • RO1:

    Research Plan must be <=25 pages

    • Specific Aims: 1

    • Background: 3

    • Preliminary Studies: 6-8

    • => Research Design/Methods: 13-15

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Informative Writing

Target readers’ understanding

  • Inform the reader

  • Explain what is difficult to understand

  • Say only what needs to be said

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  • Overly ambitious research plans

  • Contingent Specific Aims

  • Complex, emerging techniques without establishing familiarity or including expert

  • Too little detail on data analysis

  • Under-powered studies

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Summary: Successful Research Design and Methods

  • Bright idea

  • Well developed and clearly described methods

  • Appropriate data analysis

  • Large enough sample size

  • Plenty of time to do the work

  • Only minor limitations

  • Clear pathway to strong conclusions