Preparing EdgeR - ccsstudentmentors/tutorials GitHub Wiki

Step 1: Download the files produced by HTSeq-count for each of your samples (this was also the last step of the counting reads section). Put these files in a working directory on your computer that will be convenient to work in. I am just going to call it: C:\RNASeq\ReadCounts\ Go ahead and make additional folders there for our eventual output:

C:\RNASeq\EdgeROutput\
C:\RNASeq\EdgeRDEGenes\

Step 2: Download and install R: https://cran.r-project.org/bin/windows/base/
Step 3: Donwload and install R-Studio: https://www.rstudio.com/products/rstudio/download/
Step 4: Launch R-Studio. Move to your RNA-Seq directory with the following command:

setwd('C:/RNASeq/')

Note: no, that isn't a typo, R uses forward slashes to separate folders even in Windows Step 5: Install biocLite (the installation/updating software for bioconductor):

source('http://bioconductor.org/biocLite.R')

If you are asked to update all, some, or none of the dependent packages, type 'a' and then hit the 'enter' key to update all of them
Step 6: Install EdgeR

biocLite('EdgeR')

If you are asked to update all, some, or none of the dependent packages, type 'a' and then hit the 'enter' key to update all of them
Step 7: Load EdgeR

library(EdgeR)

Proceed to the simple EdgeR data analysis section or the EdgeR multiple-variable analysis section.
The simple analysis covers data analyses where you have three replicates of a control condition and three replicates of an experimental condition. The multi-variate EdgeR analysis script handles more advanced/complicated setups.