RNASeq: Differential gene expression analysis

Introduction

After mapping reads to a reference sequence and obtaining the count data, the differential gene expression analysis will determine whether differences in count data are likely to be reflect true differences in sample conditions. The details of performing this analysis are described in the two tutorials listed here.

Using R on Abel

The INFBIO9120 tutorial is using the R library DESeq for gene expression analysis. The newer library DESeq2 is used in the second tutorial. Both of these libraries are available on Abel.

In order to start R and load the DESeq (or DESeq2) library on Abel, type:

module load R

R

library(DESeq)

The second tutorial is using the pasilla dataset. This dataset is not part of the R installation on Abel. To install it, use:

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

biocLite("pasilla")