Workshop
Data Analysis 3: Biomedical sciences - Your data analysis
Introduction
In this workshop you will use the tools you used in the previous workshop (and before!) to analyse the data you have collected. You will provide some key pieces of information for the class data set.
Exercises
Getting started on your own analysis
🎬 Open the RStudio Project you created in the Consolidation exercise from week 2.
🎬 If you have not already done so, save your data files to the project. Are the file names going to be easy for you to work with? Remember that we used the file names to label to rows with their treatment (Media, LPS or ECOLIGreen) and antibody (ISOTYPE or TNFAPC) so if you do not match the names you will need to redesign the code appropriately. It is easier to rename your files!
🎬 Open your R script and begin to analyse your data.
Data for the class dataset.
You need to provide the following information for the class dataset:
group_name A name for your group. Take care not to use a name used by others. Take care to use the exactly the same name for each of your rows
cell_treatment
One of MEDIA, LPS or ECOLIGreenantibody
One of ISOTYPE or TNFAPCn
The number of cells in sample after flowAI cleaningn_live
The number of cells in sample after flowAI cleaning and removing dead cells/debris (“gating”) (i.e., the % live cells)perc_live
The % of cells in sample after flowAI cleaning and removing dead cells/debris (“gating”) (i.e., the % live cells)apc_cut
threshold for logicle transformed TNFa_APC_Lin. This should be the same for all your samples and indicates the level at which cells are postive for TNF-α positivemean_apc
Mean fluorescence intensity of the logicle transformed TNFa_APC_Lin in the TNF-α positive cellsn_pos_tnfa
Number of TNF-α positive cellsperc_pos_tnfa
Percent of live cells that are TNF-α positive
Enter these in the BIO00066I Biomedical Sciences class data
Some columns are required for the class analysis. Other columns help you get to the required values and help others determine the reliability of your data.
How to change the name of an RStudio project.
You will need to rename your RStudio Project to your exam number before you submit. You can change the name of an RStudio project by:
closing the project
renaming both the project folder and the
.Rproj
file.
Independent study following the workshop
The Code file
This contains all the code needed in the workshop even where it is not visible on the webpage.
The workshop.qmd
file is the file I use to compile the practical. Qmd stands for Quarto markdown. It allows code and ordinary text to be interweaved to produce well-formatted reports including webpages. View the Qmd in Browser. Coding and thinking answers are marked with #---CODING ANSWER---
and #---THINKING ANSWER---
Pages made with R (R Core Team 2024), Quarto (Allaire et al. 2022), knitr
(Xie 2024, 2015, 2014), kableExtra
(Zhu 2024)