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News: J-Express 2011 released. Download from jexpress.bioinfo.no
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1  J-Express / Forum / Re: out of memory error on: April 15, 2015, 10:13:16 AM
Hi Stijn,

Please see the "broken installer" topic in this forum, that gives instructions on manually installing the exec.properties file that lets you customize settings such as java memory limits that J-Express relies on.

Increasing the default max memory limits should improve the performance. Clustering of 37000 transcript profiles is still challenging for brute force approaches like hierarchical clusteing ( matches all vs all in every iteration). Filtering out for instance very flat/non-varying and thus non-informative transcript profiles (if you are looking for correlation pattern using a correlation based distance meassure), is often adviced. This you can do in J-Express under  the Dataset tab, Create sub dataset, selecting between different filtering criteria/measures, when you have selected the dataset to filter down from in the Project window.

Kjell Petersen
The Norwegian Bioinformatics platform
2  J-Express / Forum / Re: Cannot run J-Express 2012 on: March 02, 2015, 08:39:56 AM
Hi all, updating this post for later viewers:

The link is working now, may have been temporarily down at the time when Jan Roger tried to access it.

3  J-Express / Forum / Broken installer on: December 02, 2014, 10:08:49 AM
The J-Express installer is partly broken:

- The second last page in the progress of installing J-Express is blank.
- Press exit instead of next, all the install work is done.
- If you click next, the window will hang. If you "X" this window, it's ok, all the install work is done

You may then start J-Express by either:
- find the Launch.jar file in the directory you intstalled J-Express, and double click it to start it with java
- type "java -jar Launch.jar" from a command-line terminal after you've navigated to the directory containing the Launch.jar file.

Remember to add your license info under "Settings | License information" inside J-Express. Restart for this to take effect.

The installation will then run with default properties. If you would like to change them:
- Download this file to your J-Express directory :
   - Mac/Linux: http://www.ii.uib.no/~kjellp/jexpress/default.exec.properties.ml
   - Windows: http://www.ii.uib.no/~kjellp/jexpress/default.exec.properties.w
- Rename it to exec.properties
- Edit it with a text editor and replace all occurrences of <JExpress 2012 install dir> with your actual path to your J-Express installation directory. (Replace <> signs also, should not be there after the edit).
- Change the max and min memory settings to your likings (rule of thumb: not set max to more than 50% of your computers available memory).
- Restart J-Express for settings to take effect.

Kjell Petersen
Norwegian Bioinformatics Platform helpdesk
CBU - University of Bergen
4  J-Express / Forum / Re: Cannot run J-Express 2012 on: June 21, 2013, 02:44:38 PM
This is due to the latest Oracle Java security release where they've altered the API to start command line processes, which causes directory names with a space in it to fail. And for J-Express default installation in Windows being under "Program Files", this causes J-Express start-up to fail.

Phillipe fixed his installation by downgrading java to an earlier release/version. The security patch is done both on Java 6 and 7.

We've compiled an alternative Launch.jar file that can be used instead of the original one, that will use another method in the Java API that will handle spaces in directory names. Simply replace your Launch.jar file in the J-Express installation directory with this file: http://www.ii.uib.no/~kjellp/jexpress/Launch.jar

Kjell Petersen
Norwegian Bioinformatics platform
jexpress.bioinfo.no support team
5  J-Express / Forum / Re: FSS P-values on: April 18, 2012, 03:14:34 PM
Hi ebent,

Correct FSS p-value comes from the standard t-test analysis. For sample groups, this makes sense only for pairwise comparisons (or possibly single group in case of ratio data with the pairwise comparison being implicit). Thus J-Express don't compute FSS statistics if you select more than two sample groups. ANOVA on the other hand is a more suitable approach for analysing differences over more than two groups. I'm not sure what J-Express would do in case of 1 sample in a group, but I'm definitely sure that it doesn't make sense to do this analysis Smiley

Yes, the p-values are nominal p-values for each gene tested individually, and needs to be corrected for multiple testing.


6  J-Express / Forum / How to change the scales on a plot ? on: November 23, 2005, 12:43:36 PM
If right clicking a plot I get the properties dialog, and find the min and max values boexes for both axes, but they are greyed out...?

The same goes for the tick box: Force End Points

Are there any way to activate these options ?

When plotting only not filtered data it would be nice to scale the axes to fit the shown data only, and exclude the empty area at the lower left.

7  J-Express / Jython Scripting / Re: Correlation calculations in JE? on: October 04, 2005, 11:02:42 AM
In the Genepix-suite: Add process -> Other -> new jython Script-> paste the following script:

#description: Calculate the correlation between two channels or two single-channel arrays

from expresscomponents.MissingValues import Stat

ch1 = array.getValues(0)
ch2 = array.getValues(1)

print Stat.corr(ch1,ch2)

The script works for 2-channel data, but fails for 2 1-channel arrays (Exception at ch2 = getValues(1)). I've tried with the two arrays side-by-side as replicates and as seperate arrays one-below-the-other in the experiment design.
8  J-Express / Jython Scripting / Correlation calculations in JE? on: September 29, 2005, 10:58:32 AM

Are there any way I can calculate correlations between the intensitities in the 2 channels of a 2 channel system, and between 2 arrays in a 1 channel system, within JE?

Either at the Spotpix level or higher up (if intensities are not transformed into ratio/logratios) ?

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