To do before the first class

Download softwares, create project and create data table

Karen Cristine Goncalves, Ph.D.

2023-08-01

First things first, download and install:

Create a project named "R_classes"

By creating a project, you can be sure that your input and output will all be in the same folder (called a directory in programming)

Follow one of the tutorials below to create a project:

  • Follow the instructions here
    • if you are lazy like me, just look at the figures in the article
  • Watch the following video to see how to create a project

Prepare the working directory (project folder)

Create 4 folders in the project folder

  1. Inputs
  2. Outputs
  3. Plots
  4. Scripts

Note: try not to use non-english symbols, spaces or dashes ("-") in file or folder names

Prepare the input table

If you have data you wish to work on (be it: fluorescence measured in FACS or microplate, concentration of protein, OD of bacteria/algae, gene expression levels), prepare the table as follows:

SampleA_rep1 SampleA_rep2 SampleA_rep3 SampleB_rep1 SampleB_rep2 SampleB_rep3
Measurement_1 value value value value value value
Measurement_2 value value value value value value
Measurement_3 value value value value value value
Measurement_4 value value value value value value
Measurement_5 value value value value value value
Measurement_6 value value value value value value

Where:

  • SampleA/SampleB are the different treatments and rep_1/2/3 are the biological replicates
  • Measurement1/2/3/4/5/6 are the proteins/genes measured (several repetitions of the same assay go one per line)