Group Projects

For this group activity, the odd-numbered groups will be analyzing the data from Research Project A, and the even numbered groups from Research Project B.

Example notebooks

Joseph and Laura tried their hands at the group projects as well. Take a look at the notebooks below and see what you think of their attempts.

Research Project A - Does eating yogurt change the vaginal microbiome?

Study Description

This is a randomized controlled trial to study whether yogurt consumption has an effect on the microbiome post antibiotic treatment. Absolute abundance of bacteria (in gene copies / mL) was measured by 3 qPCR assays (for total, L. crispatus, L. iners). Cytokine levels (in ug/mL of vaginal fluid) were also measured by Luminex. We also looked at the number and type of immune cells in the vagina using Flow Cytometry. Data was collected at two timepoints, pre and post antibiotic treatment.

Primary Aim

To investigate whether the consumption of yogurt influences microbiome composition after antibiotics treatment.

Research Project B - Does birth control change inflammation during menses?

Study Description

This is an observational study to evaluate the relationship between birth control and vaginal inflammation In response to menstruation. Absolute abundance of bacteria was measured by 3 qPCR assays (for total Bacteria, L. crispatus, L. iners). Cytokine levels (in ug/mL of vaginal fluid) were also measured by Luminex. We also looked at the number and type of immune cells in the vagina using Flow Cytometry. Data was collected at four timepoints; before, at the start, the end, and after menstruation.

Primary Aim

To investigate whether taking birth control is associated with vaginal inflammation throughout the menstrual cycle.

Wednesday PM Session

Session Structure
- 1:30-2:00:
- Read Research Project description below for your project
- Download project data files and put them in your folder
- Make a new .qmd file for this project.
- 2:00-3:00
- Load the demographic table into an R tibble.
- Make notes about what each column name is and what it means.
- Examine and note basic parameters (using R commands) - number of participants, visit structure, number of features measured for each, type of data measured (binary, categorical)
- Plot a histogram of all numeric features (eg, distribution of age) and bar plots for counts of categorical variables (eg. how many female).
- 3:00 - 3:30 - Break
- 3:30 - 5:00
- Preproccessing the data to prepare for tableone
- Use tableone for the dataset

Thursday PM Session

Yogurt Groups

Tomorrow after lunch, you will present some results to a neighboring group. The presentation will be ~30 minutes long, and at least 3 people from your group should speak on a section.

You want to present to them table 1, explain the study, explain your research question, and show visualizations and/or stats to explain your findings. The format will be a rendered qmd document (which will be an html file). You can use the module 6 corrected qmd as a template (now available from module 6).

In this session:

  • Load all 4 tables and familiarize yourself with the dataset, especially in the context of the research aim
  • Translate the research aim into a statistical hypothesis. Justify the choice.
  • Join qPCR with demographic data (wide/long)
  • visualization (boxplot) of qPCR variable levels by study arm
  • do you need to transform this data in any way? Justify the choice.
  • define a metric to characterize (justify choice).
  • Specify lower and upper limits of detection by looking at the highest and lowest values of each qPCR value
  • longitudinal visualization of chosen cytokine for all participants.
  • Extra Challenge - try incorporating the data from the luminex data table. Pick 1-3 cytokines that seem to be detected in many samples to analyze in combinatino with the qPCR and demographic variables.

Overall, come up with and answer two main questions, one comparing one arm vs the other, and one comparing a demographic factor, looking at the qPCR variables. For extra challenge, also describe some relationships between the qPCR variables and cytokines.

Birth Control Groups

Tomorrow after lunch, you will present some results to a neighboring group. The presentation will be ~30 minutes long, and at least 3 people from your group should speak on a section.

You want to present to them table 1, explain the study, explain your research question, and show visualizations and/or stats to explain your findings. The format will be a rendered qmd document (which will be an html file). You can use the module 6 corrected qmd as a template You can use the module 6 corrected qmd as a template (now available from module 6).

In this session:

  • Load all 4 tables and familiarize yourself with the dataset, especially in the context of the research aim
  • Translate the research aim into a statistical hypothesis. Justify the choice
  • Join cytokine with demographic data
    visualization (boxplot) of cytokine levels by study arm
  • Pick one to three cytokines (justify choice). Specify lower and upper limits of detection
  • Longitudinal visualization of chosen cytokines for all participants
  • Extra Challenge - try incorporating the data from the flow_cytometry data table. Pick a population (or a ratio of two populations, such as CD4+/CD3+) of immune cells that seem to be associated with some cytokine and demographic variables.

Overall, come up with and answer two main questions, one comparing one arm vs the other, and one comparing a demographic factor, looking at the cytokine variables. For extra challenge, also describe some relationships between the flow cytometry variables, and cytokines, and longitudinal patterns.