Gene differential expression using DEGseqΒΆ

Author:Likit Preeyanon
Date:June 7, 2010

First, install R and related programs:

%% apt-get -y install zip xdg-utils libxss1 tcl8.5 tk8.5
%% curl -O http://cran.mtu.edu/bin/linux/debian/lenny-cran/r-base-core_2.11.1-1~lennycran.0_i386.deb
%% dpkg -i r-base-core_2.11.1-1~lennycran.0_i386.deb
%% apt-get install gfortran

Then, run R on your machine:

%% R

You should see this (if not, scream loudly):

R version 2.11.1 (2010-05-31)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

>

Then within R, install DEGseq package:

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

It will take about 10 mins to install all dependencies. Go get some coffee and relax.

When installation is done. Import DEGseq library to R:

> library('DEGseq')

You will see a list of required packages.

The data for this tutorials should be in ~/ngs-course/data/expression_data.txt.

Now, we will load the expression data into R:

> geneExpMatrix1 = readGeneExp('~/ngs-course/data/expression_data.txt', header=FALSE, sep='', geneCol=1, valCol=2)
> geneExpMatrix2 = readGeneExp('~/ngs-course/data/expression_data.txt', header=FALSE, sep='', geneCol=1, valCol=3)

You can explore you data:

> write.table(geneExpMatrix1[1:10,], row.names = FALSE)

You will see the first ten records of the first dataset:

        "V1" "V2"
"SPU_000003" "67"
"SPU_000005" "3"
"SPU_000007" "5"
"SPU_000008" "41"
"SPU_000010" "2"
"SPU_000011" "15"
"SPU_000012" "29"
"SPU_000013" "232"
"SPU_000014" "2"
"SPU_000016" "8"
"SPU_000017" "10"

Now, run DEGexp function to analyze gene expression.

We will use method “MARS” and save all output to ~/expData:

> DEGexp(geneExpMatrix1 = geneExpMatrix1, geneCol1 = 1, expCol1 = 2, groupLabel1 = 'unfed', geneExpMatrix2 = geneExpMatrix2, geneCol2 = 1, expCol2 = 2, groupLabel2 = 'fed', method = 'MARS', outputDir='~/expData')

and wait patiently...until you see:

Done ...
The results can be observed in directory:  ~/expData
>

Hooray!! Now you can quit R:

> q()

It will ask you if you want to save your data, press yes if you want to use your data again in R.

Then you go to ~/expData/:

> cd ~/expData/
> ls -l

You will see two files and 1 directory:

drwxr-xr-x 2 root root    4096 Jun  7 16:04 output
-rw-r--r-- 1 root root    4565 Jun  7 16:05 output.html
-rw-r--r-- 1 root root 2200620 Jun  7 16:05 output_score.txt

Here is what you can do:

  1. Open output.html on Firefox and you’ll see a nice report.
  2. Import output_score.txt to Excel.
  3. You can find all plots in output directory.

Note, to download ~/expData directory to your computer:

%% tar czf expData.tar.gz ~/expData

LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.
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