Bayesian Analysis of Variance for Microarrays

Frequently asked questions

  1. How can I check if I installed java correctly (or if I need it)?
  2. I just installed java. How can I can check where the install is located?
  3. Where should I install java?
  4. I noticed that Sun has J2SE 5.0 JRE. Can I install this instead?
  5. I got an error during licence verification with a license key containing special XML characters.
  6. Do you support legacy OS, Windows 2000 operating system?
  7. Mac OS X issue: during installation, when clicking the install file, an error message says the .command file could not open.
  8. Mac OS X issue: during installation, when clicking the install file, an error message says "No Java Runtime Environment(JRE) was found on this system."

  1. How can I check if I installed java correctly (or if I need it)?

To check the validity of the install open up a Command Prompt Window ("Program Files -> Accessories -> Command Prompt") and type "java -version". The system should respond with "1.4.x_xx".

In fact we encourage users to do this step before installing the JRE, because they may have the JRE on their machine and not know it.


  1. I just installed java. How can I can check where the install is located?

Go to "Program Files -> Search -> For Files or Folders" and click on "All files and folders" on the left hand side pane of the window and type "java.exe" in the "All or part of the file name" text box.


  1. Where should I install java?

The default and suggested install location is:

C:\Program Files\Java\j2re1.4.x

It is important for the user to choose a typical location. The BAMarray installation searches several locations, but not the entire or all hard drives, which can lock up a machine for minutes, especially in a networked environment.


  1. I noticed that Sun has J2SE 5.0 JRE. Can I install this instead?

No, install J2SE 1.4.x. We do not support 5.0 JRE at this time.


  1. I got an error during licence verification with a license key containing special XML characters.

< less than
> greater than
& ampersand
' apostrophe
" quotation mark

are currently not handled correctly by the web site. The customer will experience an error during license verification. The work-around in this situation is to delete the above characters appearing in the <key id="..."> and <key customer="..."> fields in the license key file. Do not modify any other fields in the license key file. Make sure you save a copy of the original license key file before attempting to modify it.


  1. Do you support legacy OS, Windows 2000 operating system?

We do not support the product on the legacy OS, Windows 2000. However, a few customers have attempted to install the product on this platform and have encountered some issues during the process. We do have a manual work-around for this situation. Please contact technical support.


  1. Mac OS X issue: during installation, when clicking the install file, an error message says the .command file could not open.

When installing under MAC OS X, double clicking the install file, BAMarray_mac_2_0_1.command, may give the error that the .command file could not open. Simply change to the directory where the install file is located and give the file execution permission. For example, if the install file is on your Desktop:

Go > Utilities > Terminal
Press Enter
cd ~/Desktop
chmod aou+x BAMarray_mac_2_0_1.command


  1. Mac OS X issue: during installation, when clicking the install file, an error message says "No Java Runtime Environment(JRE) was found on this system".

Our JVM consistency check in BAMarray is fine in that we allow Java 1.4.X or 1.5.X, but the InstallShield package, that needs a JVM to bootstrap itself, checks for JRE's in a limited number of locations.

Change to the directory where the install file is located. For example, if the install file is on your Desktop:

Go > Utilities > Terminal
Press Enter
cd ~/Desktop

Now set your JAVA_HOME environment variable. For example (make sure everything is one one line):

setenv JAVA_HOME /System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home

Now install by explicitly indicating where your Java is located:

./BAMarray_mac_2_0_1.command -is:javahome $JAVA_HOME

This solution will work for PowerPC-based Macs. For intel-powered Macs please contact Technical Support for an alternate workaround.