Integrated analysis of Cross-platform MicroArray and Pathway data
Frequently asked questions (FAQ)
- Where can I get help for a certain component/ option/ checkbox/ etc.?
- Is an internet connection required to run InCroMAP?
- Where can I get the latest version?
- Where can I get more information on the pathway translations?
- I am behind a proxy server and keep getting the error "could not retrieve list of organism from KEGG".
- The application crashes, saying "java.lang.OutOfMemoryError: Java heap space".
- Which Java version must be installed on my computer to launch InCroMAP?
- Why does InCroMAP not start on my Mac with Mac OS prior to 10.6 Update 3?
- How can I change the look and feel of the application (colors and shapes)?
- Which organisms are supported?
- Can I import other microarray data types than the mentioned four?
- Is one node in a pathway always one gene?
- How can I save or export a picture/ table/ etc.?
- Error message while visualizing data in the pathway: no node matches the input data?
- No targets could be annotated to my miRNA data?
- What does "Observation" or "Signal" mean?
- Is it possible to import data directly from the GEO database?
- Is it possible to fix missing links in pathways?
General technical questionsdownloads section. KEGGtranslator.
I am behind a proxy server and keep getting the error "could not retrieve list of organism from KEGG".Java provides its own means of configuring proxy servers for the JVM. Windows users may configure their proxy server as described here. Users of all operating systems can specify proxy hosts as command-line options for the JVM as described by Oracle in this article. If you require a proxy server for making connections to the internet, please start InCroMAP from the command-line with the following syntax:
java -Xms256m -Xmx1024m -Dhttp.proxyHost=MYPROXYHOST -Dhttp.proxyPort=MYPROXYPORT -Dftp.proxyHost=MYPROXYHOST -Dftp.proxyPort=MYPROXYPORT -DsocksProxyHost=MYPROXYHOST -DsocksProxyPort=MYPROXYPORT -jar InCroMAP.jar
Where -Xmx specifies the amount of memory available to the application and InCroMAP.jar needs to be replaced with the actual JAR file name of InCroMAP (e.g., InCroMAP1.3.0.jar). Each occurrence of MYPROXYHOST should be replaced with the name of your proxy (e.g., webcache.mydomain.com) and each MYPROXYPORT must be replaced with the port number of your proxy (mostly 80 or 8080).
There are also parameters to specify the proxy username and password (-Dhttp.proxyUser and -Dhttp.proxyPassword). Please see several other resources for more information.
Starting the application / common errors and exceptionshere to download of the latest Java version.
Exception in thread "AWT-EventQueue-0" java.lang.NoClassDefFoundError: com/apple/eawt/AboutHandler
at java.lang.ClassLoader.defineClass1(Native Method)
The interface com.apple.eawt.AboutHandler was introduced to Java for Mac OS X 10.6 Update 3. If you have an earlier version of Mac OS or Java, please update your OS or Java installation. Also see the Mac OS documentation about the AboutHandler for more information. On a Mac you can update your Java installation through the Software Update menu item in the main Apple menu.
java -Xms256m -Xmx1024m -Dswing.defaultlaf javax.swing.plaf.metal.MetalLookAndFeel -jar InCroMAP.jar
will start InCroMAP using Java's default look and feel. A list of other look and feels can be found here.
Content related questions / errors / exceptionsGEO2R. This can be used perfectly to export data from GEO into InCroMAP. You can call it either directly from the given URL or by clicking on the "Analyze with GEO2R" link that is shown at the bottom of each GEO series. After successfully using this tool (at the top of the GEO2R page is a link to a tutorial video) you can click the "Save all results" link and store the result somewhere on your computer. You maybe need to use the "save page as" function of your browser. Afterwards, please open this file in InCroMAP, assign observations to all p-values and fold changes (logFC) and use the gene symbols as identifiers.
Missing links in signaling pathways unfortunately cannot be restored. However, by underlying the original KEGG image in the background, they can be made visible to the user (ensure option "Show KEGG picture in graph background", which can be found in "Preferences", "Graph options" is selected).