- The Biomedical Data guide is designed to connect you to Biomedical Research resources available to you via UM Libraries.
- This guide provides information about statistical tests, finding data sources, data visualization resources, and more.
- You can access the learning resources offered in my workshops that include topics on SPSS, R, Tableau, and Meta-Analysis.
- This guide is constantly evolving and contact me if you find a tool or learning resource that could be included here.
Data visualization is the visual presentation of data and an essential step in data analysis.
As the image below illustrates, a good visualization should be the intersection of data, function, and design.
Visual elements like graphs, maps, tables, and plots help the audience identify trends, patterns, and distributions in the data. Data visualization is useful in converting complex data sets into meaningful information that the user quickly understands. Researchers in biomedical fields collect large amounts of data that are becoming increasingly complex.
- Visualization of Biomedical Data
- Better Data Visualizations: A Guide for Scholars, Researchers, and Wonks
- Designing Data Visualizations
- A Practitioner's Guide to Best Practices in Data Visualization
- Beginning Data Science in R: Data Analysis, Visualization, and Modelling for the Data Scientist
- Tasks, Techniques, and Tools for Genomic Data Visualization
How do we create a meaningful visualization?
- Know your audience
- Choose the right graph/table
How to choose the right graph for your data.
The data visualization catalogue.
Declutter-story telling with data.
Charts Do's and Don'ts.
- Focus attention
Practical Rules for Using Color in Charts.
Choose Appropriate Visual Encodings.
Tableau offers free one-year licenses to students. Click to request your license.
Tableau online resources are a great way to start learning the software.
R offers additional packages to cater to any visualization task.
ggplot2: Creates custom plots. Refer to Cookbook for R to learn ggplot2.
GGally: Creates correlation matrix and survival plots.
gplots: Creates heat maps, Venn diagrams.
leaflet: Builds interactive maps.
Click to learn more about R packages.
AHRQ Research Data Infographics
Cochrane Handbook for Systematic Reviews of Interventions, version 6.2
Meta-analyses are a subset of systematic reviews and play a fundamental role in evidence-based healthcare. It comes at the top of the evidence-based medicine pyramid.
- Combining studies in a meta-analysis can increase the overall statistical power to detect an effect.
- Help make a valid decision about intervention and identify the reasons for the variation.
- Settles controversies arising from apparently conflicting studies or evaluates new hypotheses.
- Search the published literature: Cochrane Library, Campbell Collaboration
- Registered as an ongoing review: Prospero, Cochrane
It is important to obtain all relevant studies to avoid bias and include all evidence in the study. The search requires searching multiple databases and gray literature.
Inclusion/exclusion criteria are established before conducting the literature search to set boundaries for the review.
Eg: Study is restricted to a certain age group, symptoms experienced by the participants, location, written language
- Dichotomous variables (e.g., deaths, patients with at least one stroke)
- Count data (e.g., number of strokes)
- Continuous variables (e.g., blood pressure, pain score)
- Sample size
- Sensitivity, specificity
- Survival data
Statistical analysis is a two-step process.
- First stage: summary statistic is calculated for each study to describe the observed intervention effect.
- Second stage: A summary (combined) intervention effect estimate is calculated as a weighted average of the intervention effects estimated in the individual studies.
- Fixed effect model
- assumes all studies are estimating the same (common) treatment effect.
- Random effects model
- assumes observed estimates of treatment effect can vary across studies.
Source: Introduction to SAS. UCLA: Statistical Consulting Group.
- MEDLINE - Biomedical literature database
- CENTRAL - Cochrane Central Register of Controlled Trials
- CINAHL - Cumulative Index to Nursing and Allied Health Literature
- Embase - Biomedical and pharmacological (including MEDLINE titles)
- PsycInfo - Psychological, behavioral, social, and health sciences research
- ClinicalTrials.gov - database of clinical studies conducted around the world
- Web of Science, Scopus, Google Scholar
- Cochrane Interactive Learning: Calder medical library offers access to the online course.
- Revman training videos
The site contains health-related data sets on various topics, including community health, medical devices, substance abuse, and hospitals. Data sets are organized by the topic. Some data sets are readily available, and in other cases, you will be directed to another site.
The site is home to more than 350,000 research studies conducted in more than 200 countries. The U.S. National Library of Medicine runs this resource.
The site offers a comprehensive guide on how to customize a search.
NCHS is a part of the Centers for Disease Control & Prevention (CDC) and provides data and health statistics on crucial public health topics.
- Health, United States, is an annual report on trends in health statistics. It includes trend tables and figures on selected topics such as mortality, life expectancy, causes of death, and health care expenses, among other topics. https://www.cdc.gov/nchs/data/hus/hus18.pdf
- FastStats is a site within the NCHS that offers quick access to data, statistics, and reports on specific health topics. The topics are organized in alphabetic order and will direct you to more resources on the topic.
- The National Vital Statistics System provides access to most of the data on birth and deaths in the United States. There are links on the webpage that links to statistical reports, data sources, and data visualizations.
Cancer Query Systems - allows access to cancer data stored in an online database. The web-based interface is easy to use and retrieve statistics using a query-based system.
SEER*Stat - The data downloaded can be analyzed using the SEER* Prep and SEER*Stat statistical software.
Please refer to the webpage for installation instructions and tutorials.
NDA collects and stores data from and about human subjects across many research fields. It holds data collected by researchers funded by the National Institute of Alcoholism and Alcohol Abuse (NIAAA) and autism researchers. Also, it stores data from the Adolescent Brain and Cognitive Development Study, the Human Connectome projects, and the Osteoarthritis Initiative.
The website offers access to national, state, and regional data collected via the National Survey of Children’s Health (NSCH). The survey collects data on mental health, dental health, development, and many other child health indicators to improve child, youth, family, and community health and well-being. You can submit a data request to access the raw data or use the interactive query base system to search the data.
The survey collects data about the American public’s knowledge of, attitudes toward, and use of cancer- and health-related information. The data sets help researchers identify how adults use different communication channels to understand and obtain health-related information. HINTS data are free to download and analyze.
NTDBRDS is maintained by the American College of Surgeons and is the most extensive collection of U.S. trauma registry data. The researchers must submit an online request to obtain the data sets that are available at a cost.
HCUP's databases contain information on inpatient stays, emergency department visits, and ambulatory care.
Nationwide HCUP Databases
National Inpatient Sample (NIS)
- Kids’ Inpatient Database (KID) - KID Database Documentation
- Nationwide Ambulatory Surgery Sample (NASS) - NASS Database Documentation
- Nationwide Emergency Department Sample (NEDS) - NEDS Database Documentation
- Nationwide Readmissions Database (NRD) - NRD Database Documentation
State-specific HCUP Databases
- State Inpatient Databases (SID) - SID Database Documentation
- State Ambulatory Surgery and Services Databases (SASD) - SASD Database Documentation
- State Emergency Department Databases (SEDD) - SEDD Database Documentation
HCUPnet is a part of the HCUP project and offers a free on-line query system to access data on inpatient stays (NIS, KID, SID, and NRD), emergency department visits (NEDS, SEDD, SID), and community (SID). You create an analysis set-up by clicking on “Create new analysis.” Once the analysis is completed, it can be customized using the “My analysis” menu.
- Assumptions: Normal distribution (Shapiro-Wilk test), homogeneity of variances (Levene's test), independence of observations, no outliers.
- Example: Compare the means of two independent samples.
- SPSS Demo
- Assumptions: Normal distribution (Shapiro-Wilk test), homogeneity of variances (Levene's test), independence of observations, no outliers
- Example: Compare the means of two dependent samples.
- Assumptions: Normal distribution (Shapiro-Wilk test), homogeneity of variances (Levene's test) independence of observations, no outliers.
- Example: Compare independent sample means for more than 2 groups. Post Hoc - if equal of variances assumed select Tukey test. Otherwise, select Games-Howell.
- Assumptions: Normal distribution (Shapiro-Wilk test), homogeneity of variances (Levene's test) independence of observations, no outliers, sphericity (Mauchly’s test).
- Example: Compare means of 3 or more groups with the same participants.
- Assumptions: Association between the two variables is linear, Normal distribution (Shapiro-Wilk test), no outliers.
- Example: Examine the linear association and direction between two continuous variables. It takes a value between +1 to -1.
- Assumptions: There should be a linear relationship between the 2 variables, no significant outliers, independence of observations, Normality.
- Example: Examine the linear association between a continuous outcome variable, and one or more independent variables.
Continuous or ordinal Data
- Assumptions: Independence of observations, distributions of the independent variable should have the same shape, independent variable consists of two categorical groups.
- Example: Compare the means of two independent samples when the normality assumption is violated. (alternative to an independent t-test)
- Assumptions: Independent variable consists of two categorical groups, dependent variable measured at the ordinal or continuous level, distributions of the independent variable should have the same shape.
- Example: Compare the means of two dependent samples when the normality assumption is violated. (alternative to the dependent t-test)
- Assumptions: Independence of observations, independent variable consists of two or more categorical groups.
- Example: Compare independent sample means for more than 2 groups when the normality assumption is violated. (alternate to ANOVA, an extension of Mann-Whitney U test)
- Assumptions: A group is measured 3 or more times, random sampling.
- Example: Compare means of 3 or more groups with the same participants when the assumptions of ANOVA with repeated measures are violated or the dependent variable measured is ordinal. (alternate to ANOVA with repeated measures)
- Assumptions: There is a monotonic relationship between the two variables.
- Example: Examine the linear association and direction between continuous or ordinal variables when the assumptions have failed for a Pearson correlation. It takes a value between +1 to -1. (alternate to Pearson correlation)
- Assumptions: There is a monotonic relationship between the two variables.
- Example: Examine the association and direction between continuous or ordinal variables. Specially applied to small sample sizes and for variables with many ranks. It takes a value between +1 to -1. (alternate to Pearson correlation and Spearman correlation)
- Assumptions: Independence of observations, expected cell count assumption (expected cell counts are all greater than 5)
- Example: Compare sample proportions to check if there is an association between the categories. A residual analysis will identify the specific cells that make the greatest contribution to a significant chi-square test.
- SPSS Demo
- Assumptions: Independence of observations, if the expected cell count is less than 5 for any cell, use Fisher’s exact test.
- Example: Compare sample proportions to check if there is an association between the categories. Used for small samples.
- SPSS Demo
- Assumptions: The dependent variables should be mutually exclusive.
- Example: Check the differences on a dichotomous dependent variable between two related groups.
Other commonly used tests:
- This method is used to study the reliability of the scale used in a survey (commonly used with Likert scale questions).
- The scale ranges from 0-1. If the alpha is 0.7 or above, the measure can be considered reliable. For example, a survey was designed with 10 questions to measure if the students are happy at school.
- The questions are on a Likert scale. The researcher can survey a sample and carry out the Cronbach analysis to estimate the reliability.
- This test is used to study the inter-rater reliability when two raters are evaluating a variable on a categorical scale.
- The scale ranges from 0-1. There is no clear cut-off for a good agreement. Normally 0.6-0.8 is considered good.
- There are a few assumptions to be met before conducting the test. The categories should be mutually exclusive, the raters are independent, and the same raters evaluate all the questions.
- This test is used to study the inter-rater reliability when two or more raters evaluate a variable on a categorical scale.
- If the raters are not fixed, meaning the same 2 raters are not evaluating the questions.
- Statistical methods for the analysis of biomedical data, Woolson, Robert F.; Clarke, William R. (William Radue), New York: Wiley-Interscience, 
- Parametric and Non-parametric tests for comparing two or more groups
- Choosing a statistical test
Click here to register.
You can access the material covered in the workshops here. After going through the content, please reach out to me at firstname.lastname@example.org for assistance.
- Introduction to Tableau
- Introduction to R
- Intermediate R
- Data visualization with R
- Introduction to SPSS
- Intermediate SPSS