I seem to have solved it by following the advice of someone else on this forum: I uninstalled Java, deleted all files associated with J-Express, then reinstalled Java and then reinstalled J-Express. I didn't even need to add in the exec.properties file- it seems to have installed just fine. Whew!

Update: And then I turned my computer off and on again, and the program no longer will open. I tried putting in and altering the exec.properties file and am back to the problem I had before- when the file is preasent, the program doesn't open, no matter what memory settings I put in (and yes, I also altered the file paths to be correct). When the file is removed, the program opens but won't load data.

 

Hi- I've realized that I don't have an exec.properties file- I downloaded the one Kjell linked to and made the alteration to the file (directory path) to the install directory, and now the program doesn't open at all. If I remove the exec.properties file (by renaming it), J-Express opens but does not load data.

I've tried reinstalling J-Express by manually removing folders and re-installing, and it doesn't seem to have helped.

Liz

Here is the entirety of what is in the log file: I tried opening a file and this is what came out (below) - it looks like a configuration issue? -Liz



J-Express version: J-Express 2012 Build 119.  March 12. 2012

System properties
java.runtime.name   - Java(TM) SE Runtime Environment
sun.boot.library.path   - C:\Program Files\Java\jre1.8.0_31\bin
java.vm.version   - 25.31-b07
java.vm.vendor   - Oracle Corporation
java.vendor.url   - http://java.oracle.com/
path.separator   - ;
java.vm.name   - Java HotSpot(TM) 64-Bit Server VM
file.encoding.pkg   - sun.io
user.country   - US
user.script   -
sun.java.launcher   - SUN_STANDARD
sun.os.patch.level   -
java.vm.specification.name   - Java Virtual Machine Specification
user.dir   - C:\Users\Liz\Documents\J-express
java.runtime.version   - 1.8.0_31-b13
java.awt.graphicsenv   - sun.awt.Win32GraphicsEnvironment
java.endorsed.dirs   - C:\Program Files\Java\jre1.8.0_31\lib\endorsed
os.arch   - amd64
java.io.tmpdir   - C:\Users\Liz\AppData\Local\Temp\
line.separator   -

java.vm.specification.vendor   - Oracle Corporation
user.variant   -
os.name   - Windows 8.1
sun.jnu.encoding   - Cp1252
java.library.path   - C:\Program Files\Java\jre1.8.0_31\bin;C:\WINDOWS\Sun\Java\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\ProgramData\Oracle\Java\javapath;C:\Program Files (x86)\Intel\iCLS Client\;C:\Program Files\Intel\iCLS Client\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\Program Files\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files (x86)\Intel\OpenCL SDK\2.0\bin\x86;C:\Program Files (x86)\Intel\OpenCL SDK\2.0\bin\x64;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\;C:\PROGRA~2\TABLEC~1.01;C:\Program Files (x86)\Common Files\Adobe\AGL;C:\Program Files\Calibre2\;C:\Program Files\SASHome\Secure;C:\Program Files\SASHome\x86\Secure;C:\Strawberry\c\bin;C:\Strawberry\perl\site\bin;C:\Strawberry\perl\bin;C:\Program Files (x86)\Skype\Phone\;C:\Program Files\SASHome\Secure\ccme4;C:\Program Files\SASHome\x86\Secure\ccme4;C:\Program Files\NCBI\blast-2.2.29+\bin;.
sun.awt.enableExtraMouseButtons   - true
java.specification.name   - Java Platform API Specification
java.class.version   - 52.0
sun.management.compiler   - HotSpot 64-Bit Tiered Compilers
os.version   - 6.3
user.home   - C:\Users\Liz
user.timezone   - America/New_York
java.awt.printerjob   - sun.awt.windows.WPrinterJob
file.encoding   - Cp1252
java.specification.version   - 1.8
java.class.path   - C:\Users\Liz\Documents\J-express\;C:\Users\Liz\Documents\J-express\lib\edtftpj.jar;C:\Users\Liz\Documents\J-express\lib\freehep-export-2.1.2.jar;C:\Users\Liz\Documents\J-express\lib\freehep-graphics2d-2.1.1.jar;C:\Users\Liz\Documents\J-express\lib\freehep-graphics2d-2.1.2.jar;C:\Users\Liz\Documents\J-express\lib\freehep-graphicsio-2.1.2.jar;C:\Users\Liz\Documents\J-express\lib\freehep-graphicsio-emf-2.1.2.jar;C:\Users\Liz\Documents\J-express\lib\freehep-graphicsio-pdf-2.1.2.jar;C:\Users\Liz\Documents\J-express\lib\freehep-graphicsio-ps-2.1.2.jar;C:\Users\Liz\Documents\J-express\lib\freehep-graphicsio-svg-2.1.2.jar;C:\Users\Liz\Documents\J-express\lib\freehep-graphicsio-swf-2.1.2.jar;C:\Users\Liz\Documents\J-express\lib\freehep-io-2.0.3.jar;C:\Users\Liz\Documents\J-express\lib\freehep-swing-2.0.3.jar;C:\Users\Liz\Documents\J-express\lib\freehep-swing-2.0.4-SNAPSHOT.jar;C:\Users\Liz\Documents\J-express\lib\freehep-util-2.0.3.jar;C:\Users\Liz\Documents\J-express\lib\freehep-xml-2.1.1.jar;C:\Users\Liz\Documents\J-express\lib\freehep-xml-2.1.3-SNAPSHOT.jar;C:\Users\Liz\Documents\J-express\lib\Help.jar;C:\Users\Liz\Documents\J-express\lib\iText.jar;C:\Users\Liz\Documents\J-express\lib\jai_codec.jar;C:\Users\Liz\Documents\J-express\lib\jai_core.jar;C:\Users\Liz\Documents\J-express\lib\jas-plotter-2.2.jar;C:\Users\Liz\Documents\J-express\lib\jcalendar-1.3.2.jar;C:\Users\Liz\Documents\J-express\lib\jcommon-1.0.16.jar;C:\Users\Liz\Documents\J-express\lib\jdom-1.0.jar;C:\Users\Liz\Documents\J-express\lib\jdom.jar;C:\Users\Liz\Documents\J-express\lib\jexpress.jar;C:\Users\Liz\Documents\J-express\lib\jexpressServer.jar;C:\Users\Liz\Documents\J-express\lib\jfreechart-1.0.13.jar;C:\Users\Liz\Documents\J-express\lib\jh.jar;C:\Users\Liz\Documents\J-express\lib\jmathplot.jar;C:\Users\Liz\Documents\J-express\lib\js.jar;C:\Users\Liz\Documents\J-express\lib\jsci-core.jar;C:\Users\Liz\Documents\J-express\lib\jsci.jar;C:\Users\Liz\Documents\J-express\lib\junit.jar;C:\Users\Liz\Documents\J-express\lib\jylib.jar;C:\Users\Liz\Documents\J-express\lib\jython.jar;C:\Users\Liz\Documents\J-express\lib\MAGEHandler.jar;C:\Users\Liz\Documents\J-express\lib\MAGEMLimport.jar;C:\Users\Liz\Documents\J-express\lib\MAGEstk-2004-06-29-v1.1-compatible.jar;C:\Users\Liz\Documents\J-express\lib\mlibwrapper_jai.jar;C:\Users\Liz\Documents\J-express\lib\openide-lookup-1.9-patched-1.0.jar;C:\Users\Liz\Documents\J-express\lib\servlet.jar;C:\Users\Liz\Documents\J-express\lib\swing-layout.jar;C:\Users\Liz\Documents\J-express\;plugins\stat.jar
user.name   - Liz
java.vm.specification.version   - 1.8
sun.java.command   - jexpress.jexpress
java.home   - C:\Program Files\Java\jre1.8.0_31
sun.arch.data.model   - 64
user.language   - en
java.specification.vendor   - Oracle Corporation
awt.toolkit   - sun.awt.windows.WToolkit
java.vm.info   - mixed mode
java.version   - 1.8.0_31
java.ext.dirs   - C:\Program Files\Java\jre1.8.0_31\lib\ext;C:\WINDOWS\Sun\Java\lib\ext
sun.boot.class.path   - C:\Program Files\Java\jre1.8.0_31\lib\resources.jar;C:\Program Files\Java\jre1.8.0_31\lib\rt.jar;C:\Program Files\Java\jre1.8.0_31\lib\sunrsasign.jar;C:\Program Files\Java\jre1.8.0_31\lib\jsse.jar;C:\Program Files\Java\jre1.8.0_31\lib\jce.jar;C:\Program Files\Java\jre1.8.0_31\lib\charsets.jar;C:\Program Files\Java\jre1.8.0_31\lib\jfr.jar;C:\Program Files\Java\jre1.8.0_31\classes
java.vendor   - Oracle Corporation
file.separator   - \
java.vendor.url.bug   - http://bugreport.sun.com/bugreport/
sun.io.unicode.encoding   - UnicodeLittle
sun.cpu.endian   - little
sun.desktop   - windows
sun.cpu.isalist   - amd64

File SystemJ-Express file system -- File locations
Settings file does not exist..
Used Paths:
User path: C:\Users\Liz\Documents\J-express
User data path: C:\Users\Liz\Documents\J-express\data
Annotation path: C:\Users\Liz\Documents\J-express\resources\Annotation
Sequence path: C:\Users\Liz\Documents\J-express\resources\SEQUENCE
GO path: C:\Users\Liz\Documents\J-express\resources\GO
PLUGIN path: C:\Users\Liz\Documents\J-express\resources\PLUGINS
Libraries path: C:\Users\Liz\Documents\J-express\lib
Pathways path: C:\Users\Liz\Documents\J-express\resources\PW
Settings file: C:\Users\Liz\Documents\J-express\jexpress.cfg
Spotpix path: C:\Users\Liz\Documents\J-express\resources\EXPERIMENTS
VM memory use min (MB): 256
VM memory use max (MB): 512
File system out done
Looking for license file in C:\Users\Liz\Documents\J-express
Looking for settings at C:\Users\Liz\Documents\J-express\jexpress.cfg
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
   at jexpress.cluster.addRecentFile(cluster.java:1222)
   at expresscomponents.filehandler.loadProjectNEW(filehandler.java:1096)
   at jexpress.cluster.actionPerformed(cluster.java:2673)
   at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
   at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
   at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
   at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
   at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
   at java.awt.Component.processMouseEvent(Unknown Source)
   at javax.swing.JComponent.processMouseEvent(Unknown Source)
   at java.awt.Component.processEvent(Unknown Source)
   at java.awt.Container.processEvent(Unknown Source)
   at java.awt.Component.dispatchEventImpl(Unknown Source)
   at java.awt.Container.dispatchEventImpl(Unknown Source)
   at java.awt.Component.dispatchEvent(Unknown Source)
   at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
   at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
   at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
   at java.awt.Container.dispatchEventImpl(Unknown Source)
   at java.awt.Window.dispatchEventImpl(Unknown Source)
   at java.awt.Component.dispatchEvent(Unknown Source)
   at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
   at java.awt.EventQueue.access$500(Unknown Source)
   at java.awt.EventQueue$3.run(Unknown Source)
   at java.awt.EventQueue$3.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.awt.EventQueue$4.run(Unknown Source)
   at java.awt.EventQueue$4.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.awt.EventQueue.dispatchEvent(Unknown Source)
   at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
   at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
   at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
   at java.awt.EventDispatchThread.run(Unknown Source)

No infosNew Project

Hi, I am running JExpress on Windows 8 and have had no problem using it last year after re-installing it, but now I find that when I try to open saved projects or import tabluar data for a new project, nothing happens. For example, I see a menu for choosing a file to open, click on the file I want, the menu vanishes, and nothing happens. For tabular data, I go through the wizard and once I'm done selecting my data, I click "OK" and then the tabluar data input window vanishes and nothing happens.

Is my license expired, or something like that?

Thanks

Liz

Hello,

How do I change the colours used for heat maps? There are options for changing the size of dendograms and the rows and columns, but I can't figure out how to make the colours change to one that is easier for us to interpret.

Thanks,

Liz

Hi, I wasn't able to use J-Express- for some reason, it would not load my files (it went through the dialog but then would not actually open the files specified, or any files at all).

Last time this happened, I uninstalled it and reinstalled it. So I uninstalled J-Express, and now that I am trying to re-install it, the installer does not work. After files are unpacked, an empty dialog box comes up. There is no option on it but to click "Next" and when I do that, the installer hangs up. The process is still running, but it's not doing anything.

Help!

This is for a Windows 7 64 bit machine running Java 7 update 51.

Hi, what is the citation for J-Express? I can't seem to find this information. Is there a paper, or just the URL?

Hello, I've just lost the ability to load project files- I click "Load" and nothing happens. A dialog box that is blank opens and I have to end the process with Windows Task Manager to get the program to close, because the program becomes unresponsive.

I can't restart my computer at the  moment (another process is running). Have you come across this before and if so, how did you solve it?

Liz

Hi, I can't seem to figure out how to select many genes at once by selecting their names from a list file. I have annotation data for my genes and different subsets are interesting, and I want to place them into different groups to make analysis easier. But if I have to manually scroll through the list of genes in my data file and click each one I want as I go, I will go insane. Help!

My supervisor wants to take the raw data from my read mapping, and use SAS to look at the difference between sample groups for each gene (t-tests or ANOVA tests). This is the same data that is provided in the FSS/ANOVA table, correct? So a separate analysis with SAS is redundant, the results (P-values) can just be downloaded from the table.

I am told I need to choose one of my four sample types to serve as a reference, and look for fold changes of the other sample types relative to it- is there any way to set one group as a "baseline" or "reference" to which all other groups are relative?

EDIT: Also, what does the fold change value mean when one is using ANOVA to compare 4 groups? The largest difference among the groups?

Hi there- just making sure I understand what's happening when I use FSS analyses. If I choose several groups of samples and "P-value" as the scoring method, the P-value calculated is the one that would come from a t-test analysis of the data, calculated using the mean and variance from each sample group, right? Can the FSS be used when a group contains a single sample? In this latter case, how is the P-value calculated?

Also, if I have 53,000 genes, and data from each is analysed individually (is this what FSS does?) I still need to correct the P-value to take into account the number of tests (genes), or not?

Thanks for your help.

Thanks a bunch!

Hi, can someone give me a link to a page that describes the different options (what mathematical transformations occur) for the various options under "Create subdata" in the "Data Set" page? The top ones are obvious, but I'm not sure I understand what happens to data that is "Scale Normalized", and what exactly happens with the various High Level normalizations? I can't seem to find a page that describes this (it might be there, but I can't seem to see it). I have sequence, not microarray, data and I want to be sure that if I transform my data the transformation is appropriate.

Thanks for your help!

Liz

Hi- not a problem, just an observation: I have put a lot of data into J-Express (53026 rows of data, 15 columns), then asked it to do a correspondence analysis (after increasing memory allowance settings). It's been running now for about 16 hours, and I don't know if it's almost finished or even if the program is hung up somewhere and will never finish. It would be nice, in these instances, to have the program refresh the screen at different intervals for long calculations, and update a progress bar that will let users know how close they are to finishing an analysis. I keep checking my Task Manager (I have a Windows machine), and because I see activity, I assume the program is still running. It would be nice to know if this is something that might take days longer to run, or that might almost be finished.

Tried uninstalling and re-installing J-Express, and now everything loads perfectly. It was just an installation glitch.