Primary Aim
To investigate whether the consumption of yogurt influences microbiome composition after antibiotics treatment.
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.
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.
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.
To investigate whether the consumption of yogurt influences microbiome composition after antibiotics treatment.
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.
To investigate whether taking birth control is associated with vaginal inflammation throughout the menstrual cycle.
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
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:
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.
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:
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.