Difference between revisions of "RNASeq: Differential gene expression analysis"
(Created page with "= Introduction = After mapping reads to a reference sequence and obtaining the count data, the differential gene expression analysis will determine whether differences in co...") |
|||
| Line 1: | Line 1: | ||
| − | = Introduction | + | = 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 [[ | + | 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 [[RNASeq and differential gene expression analysis|here]]. |
= Using R on Abel = | = Using R on Abel = | ||
| Line 8: | Line 8: | ||
In order to start R and load the DESeq (or DESeq2) library on Abel, type: | In order to start R and load the DESeq (or DESeq2) library on Abel, type: | ||
| + | <div style="line-height:90%; background-color: LightGray; border-style: solid; border-width:1px; font-family:courier new,courier,monospace;"> | ||
| + | <br/>module load R | ||
| − | + | R | |
| − | |||
| − | R | ||
library(DESeq) | library(DESeq) | ||
| − | + | </div> | |
| − | + | <br/>The second tutorial is using the pasilla dataset. This dataset is not part of the R installation on Abel. To install it, use: | |
| − | + | <div style="line-height:90%; background-color: LightGray; border-style: solid; border-width:1px; font-family:courier new,courier,monospace;"> | |
| − | 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 http://bioconductor.org/biocLite.R]") |
| − | |||
| − | source("[http://bioconductor.org/biocLite.R http://bioconductor.org/biocLite.R]") | ||
biocLite("pasilla") | biocLite("pasilla") | ||
| + | </div> | ||
Revision as of 13:45, 28 May 2015
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")
