> For the complete documentation index, see [llms.txt](https://ycl6.gitbook.io/rna-seq-data-analysis/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://ycl6.gitbook.io/rna-seq-data-analysis/differential_expression_analysis_using_r.md).

# Differential expression analysis using R

In the this chapter, I will demonstrate how to use R and the Bioconductor package **edgeR** to analyze the expected counts produced by RSEM.

For reader who do not have an account on the **ALPS1** server, please check if you have access to the R environment for statistical analysis in your computer or server. If not, please download and compile the software.

Below is an example. Always check and download the latest version. At the time of writing, the latest R version v3.3.2 was released on 2016-10-31.

```
wget http://cran.csie.ntu.edu.tw/src/base/R-3/R-3.3.2.tar.gz
tar zxfv R-3.3.2.tar.gz
cd R-3.3.2
./configure
make
```

R is also available on many operating system, including Windows. Please visit its website at <http://www.r-project.org/>.