Exercises for Training Day

Purpose of the Day

• It is structured to encourage you to work through four exercises during which you will learn various skills in R.
• The Exercises illustrate and explore different skills necessary for data analysis.
• The primary objective of the day is to help you develop the skills to use R to analyse your own data.

Structure of the Day

Over the course of the day, it is hoped that you will complete one example from each of the four exercises:

• Exercise I – Scripts containing data to plot and analyse.
• Exercise II – Data wrangling before and within R
• Exercise III – Scripts that imports data, does some manipulations and calculations and generates some visualisations.
• Exercise IV – Developing a workflow for your own data

You may start at any point. For beginners, I would recommend exploring one of the scripts in Exercise I.

One script in each exercise will be explored during the day.

To execute and explore the script:

1. Cut and paste the script into the script window of R-Studio.
2. Run the script line by line and watch how the environment changes
3. Investigate the objects that have been created.
4. Play with the script to determine how the different functions affect the outcome of the graph.
5. Running parts of the layers that generate the graph is very useful.

Each Exercise is illustrated by multiple examples. You can choose any of the examples and work through more than one if that’s helpful. 

Here is the information for each Exercise.

Exercise I

1. Drawing a protein assay and calculating unknowns
2. Drawing an enzyme kinetic plot
3. Drawing a cell death curve

Exercise II

1. Wrangling in Excel
2. Wrangling with R a little
3. Using reshape package to draw six enzymology graphs with ggplot 

Exercise III

1. Making a cluster diagram with some proteomic data
2. Making a volcano plot with some proteomic data
3. Plotting a set of microscopy data from a 96 wellplate fluorescence based assay
4. Exploring functional enzymatic data (prepared by Dr SergioMartinez Cuesta)
5. Analysing a published set of microarray data (prepared by Dr Tim Stone)
6. Comparing two lists of proteins

Exercise IV - Developing YOUR OWN workflow

1. Get your data into R
2. Play with your data - visualise it!
3. Try some of the things from scripts above and apply to your own data
4. Search the web for your kind of data
5. Chat with the tutors and get some advice.

Please don't go home without trying all four exercise including having a plan for your own data.