Chipster

# CSC

# Chipster

## Software for DNA microarray analysis

### Getting started with Chipster

Chipster allows you to perform DNA microarray data analysis with the R/Bioconductor and other tools through an intuitive graphical user interface. Chipster supports all major DNA microarray platforms and, being a Java program, it is compatible with Windows, Linux and MacOS.

Launch Chipster

### Instructions

Java WebStart installs Chipster automatically. During the installation you will be asked if Chipster should be given permissions of a normal application. You have to answer "yes" in order for Chipster to start. If you find any problems during installation, see the troubleshooting section below. Prior to installation please check below that your system meets the following requirements:

- Java Runtime Environment (JRE)
- Java WebStart configured to your browser

### Troubleshooting

1. When clicking on the start-up link, the browser asks if the file "microarray.jnlp" should be saved or opened with an application

Choose application "Java WebStart" (or "javaws").

2. Java Webstart is not among the applications in the browser's prompt.

You don't have Java Web Start properly installed. You can either contact your administrator or use the following tips to fix the problem yourself.

1) Check that you have Java Runtime Environment (JRE) properly installed. You can do it by entering "java -version" at the command line. It should output installed Java version. If not, install JRE (preferrably 1.5 or newer). JRE can be found from Java download page.

2) If you have properly functioning JRE, then Java Web Start is not properly configured to your browser (during the JRE installation Java Web Start is configured automatically to Internet Explorer, Mozilla and other Netscape family browsers). Please see Java Web Start installation guide for configuration help.

3. Java Web Start tries to update Java runtime environment (JRE), but fails.

In some systems the automatical JRE update does not work. For example, the working directory for the JRE installation might be the browser's directory, where the user is not allowed to install anything. Installing JRE 1.5 or newer manually solves the problem.

4. Application crashes when selecting "yes" to "create shortcut(s)" (on Mac OS X)

Due to some issue with Java and/or Mac OS X, creating shortcuts fails on some environments. Choosing "no" should allow you to start Chipster normally. As this happens before our application starts, we unfortunately cannot do anything about it.