J-Express
Main content
J-Express is a free software for analysing gene expression microarray data.
Any type of delimited data can be imported into J-Express, in additon special importers have been created for Illumina and Agilent microarray data.
In J-Express different pre-processing options are available.
Some of the analysis methods that are available in J-Express are:
- Genset Enrichment Analysis (GSEA)
- Significance of Microarray (SAM)
- Clustering
- Principal Component Analysis (PCA)
You can download J-Express here, and create you free license here.
Some tips regarding installing J-Express:
Windows
Double-click file and follow instructions. When you are asked to choose a folder for installing the program, choose one where you have administrator rights. If your computer is managed by the university’s (or hospital’s) IT-department, please install the program on the D-drive of your computer. If you only have C-drive, please call the IT-department and have them split your disk.
MAC
Install J-Express in your Documents folder.
Generate a exec.properties file
In order to run properly J-Express need a exec.properties file. This file must be generated and put into the main J-Express folder.
Remember to change the path to your J-Express path.
Save the file using somekind of notepad. Name the file exec.properties (no other extensions).
exec.properties file (MAC version)
PathChromosomes=/Users/mbirh/Documents/J-Express2012/resources/SEQUENCE
PathSettings=/Users/mbirh/Documents/J-Express2012/jexpress.cfg
memusage=4064
memusagemin=256
PathAnnotation=/Users/mbirh/Documents/J-Express2012/resources/Annotation
PathGO=/Users/mbirh/Documents/J-Express2012/resources/GO
PathSpotPix=/Users/mbirh/Documents/J-Express2012/resources/EXPERIMENTS
PathLib=/Users/mbirh/Documents/J-Express2012/lib
PathPW=/Users/mbirh/Documents/J-Express2012/resources/PW
exec.properties file (Windows version)
PathChromosomes=D\:\\JExpress2012\\resources\\SEQUENCE
PathSettings=D\:\\JExpress2012\\jexpress.cfg
memusage=4064
memusagemin=256
PathAnnotation=D\:\\JExpress2012\\resources\\Annotation
PathGO=D\:\\JExpress2012\\resources\\GO
PathSpotPix=D\:\\JExpress2012\\resources\\EXPERIMENTS
PathLib=D\:\\JExpress2012\\lib
PathPW=D\:\\JExpress2012\\resources\\PW
Setting memory setting in J-Express
In the exec.properties file you can change the maxumim memory consumption that J-Express can use. If you have a new computer with more memory you can change these setting in the exec.properties file:
memusage=4064 (uses 4GB of memory)
Change this number to what suites your computer.
Start J-Express on a Mac
After installing J-Express in your Documents folder and generating a exec.propertiesfile you need to start J-Express (MAC version only) using the Terminal/Command line.
Open the Terminal:
cd Documents/
cd J-Express/ (remeber to use your name of the J-Express folder)
java -jar Launch.jar
J-Express course
Previous J-Express analysis courses are availble here.
In this course page you will find all presentations, exercises and files needed to go through this course by your self.