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ArrayTrack™ FAQs

Install ArrayTrack

...a microarray database, data analysis, and data interpretation tool

 

Frequently Asked Questions

 

** NEW ** Why am I having a problem with the Java7-Update 51?

 

Questions About ArrayTrack's Background and Capabilities

What is ArrayTrack™?
What is ArrayTrack’s system architecture?
Who can access ArrayTrack™?
How do I access ArrayTrack™?
What microarray data can be stored in ArrayTrack™?
Which statistical tools are available in ArrayTrack™?
How can ArrayTrack™ enhance the interpretation of microarray results?
What are the security levels available in ArrayTrack™?
How do you contact the ArrayTrack™ team (to report bugs, recommend new functions…)?

 

General Questions About Using ArrayTrack™

What are the system requirements to access ArrayTrack™?
I am a new ArrayTrack™ user. What resources are available online to help me learn how to use ArrayTrack™?
How long will it take to download ArrayTrack™?
Can ArrayTrack™ be run on Linux systems?
Can ArrayTrack™ be run on Mac OS X systems?
How can I import a dataset where expression values for several hybridizations are saved in a single spreadsheet file?

 

Questions About Installing a Local Version of ArrayTrack™

How can I obtain a copy of ArrayTrack™ to install and administer locally?
What are the requirements for running a locally installed version of ArrayTrack™?
Is installation of the R server required for performing Affymetrix probe set summarization or SAM analysis?
How will importing microarray data into ArrayTrack™ affect the space increase in the local Oracle database?
Can the database run on a SQL server database?
How can I remove the locally installed non-prompted version of ArrayTrack™ from my computer?

 

Questions About ArrayTrack™ Errors and Troubleshooting

What does this error message mean? “Connection failed: the network adapter could not establish the connection"
What does this error message I received during installation mean? “Couldn’t load jnlp file to …."
How do you open the Java console in order to allow for the diagnosis of any ArrayTrack™ problems?
What does this error message mean, "Unable to launch ArrayTrack™"?
What does this error message mean, "Error processing Cell files with R" that arises when performing Probe set conversion?
What does this error message mean, "Could not create the Java virtual machine" when trying to start ArrayTrack™?
Why is there no reponse when "Install ArrayTrack" is clicked and what do I do?

 

** NEW ** Why am I having a problem with the Java7-Update 51?

The Java 7-Update 51 won't allow our current digital certificate to pass through. We are working to solve the problem, although it may take 2-4 weeks. For now, please follow the three steps below to add links to "Exception Site List" in Java Control Panel. We are sorry for your inconvenience.
 
Step 1: Collect the links that need to be added to the "Exception Site List"

  1. From the message that reads "Unable to launch ArrayTrack™”, click the "Details" button to open the error message dialog,
  2. Click the "Exception" tab in the dialog box.
  3.  Search for the error message that reads  "#### Java Web Start Error: ".
  4. Collect all of the links that look like: "http://edkb.fda.gov/webstart/arraytrack", or file://localhost/C:/Users/Wge/ArrayTrack/AT/arraytrack.jar for later use.

Step 2: Add the links from Java Control Panel

  1. For Windows XP, click the "Java" icon to open the Java Control Panel. For Windows 7, click "Programs" then click the "Java" icon to open the Java Control Panel.
  2. Click the "Security" tab in the Control Panel and then click "Edit Site List...".
  3. In the Exception Site List, add the location http://edkb.fda.gov.
  4. Click "OK".
  5. For Arraytrack™'s Non-FDA beta version,the file-based location also needs to be added. It looks like file://localhost/C:/Users/Wge/ArrayTrack/AT/arraytrack.jar.
  6. You will also need to add the location that excludes "arraytrack.jar" to the "Exception Site List" as you did in Step 3. For example, the location to be added in this example would be "file://localhost/C:/Users/Wge/ArrayTrack/".

Step 3: Clear Java cache from Java Control Panel

  1. Under "Temporary Internet Files," click the "General" tab, and then click "Settings...".
  2. In the "Temporary Files Settings", under the "Disk Space" section, click "Delete Files...".
  3. Check all of the boxes from the "Delete Files and Applications" dialog and click "OK" to clear cached Java files.
  4. Close all of the Arraytrack™ instances that were opened and restart the application.
     

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What is ArrayTrack™?

ArrayTrack™ is toxicogenomics software for DNA microarrays. It contains three integrated components:

  1. a database (MicroarrayDB) that stores microarray data and associated toxicological information
  2. tools (TOOL) for data visualization and analysis
  3. libraries (LIB) that provide curated functional data from public databases for data interpretation

Using ArrayTrack™, you can select an analysis method from the TOOL and apply the method to selected microarray data stored in the MicroarrayDB; the analysis results can be linked directly to pathways, gene ontology and other functional information stored in LIB. 

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What microarray data can be stored in ArrayTrack™?

ArrayTrack™ handles both two-channel and one-channel microarray data in a MIAME compliant format, including Affymetrix GeneChip data. ArrayTrack™ also stores toxicogenomic data (e.g., doses, treatment schedule, chemicals).

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Which statistical tools are available in ArrayTrack™?

ArrayTrack™ provides many statistical methods and visualization capabilities for quality control, significant gene identification, and data exploring such as t-test, ANOVA, permutation t-test, false discovery rate (FDR) using the Benjamini-Hochberg method, principal component analysis (PCA), hierarchical clustering analysis (HCA), etc.

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How can ArrayTrack™ enhance the interpretation of microarray results?

ArrayTrack™ contains a rich collection of functional information on gene annotation such as chromosomal locations, GO terms, pathways, summary, and references for a gene. For gene analysis, ArrayTrack™ also provides direct hyperlinks to public genome-related Web sites, including LocusLink, Unigene, GenBank, GeneCards, OMIM, GO, KEGG, and others.

The goal of ArrayTrack™ is to provide a dynamic link between analysis results and biological interpretation. Users can easily toggle back-and-forth between biological interpretation (through individual gene, pathway, and GO analysis) on a list of significant genes and the significant-gene identification using various statistical methods. ArrayTrack™ also integrates with commercial pathway analysis tools such as Ingenuity Pathways Analysis (IPA) and PathArt.

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Who can access ArrayTrack™?

ArrayTrack™ was developed by the FDA's National Center for Toxicological Research (NCTR) and is freely available to the public. Find out how to access or obtain a copy of ArrayTrack™.

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How do I access ArrayTrack™?

  • FDA Users:
    Click here to access the software.  (NOTE: If accessing from outside FDA you will get an error message).
    You can upload your data to a database that resides at NCTR and then use the analysis and interpretation tools to better understand the data. 
  • Non-FDA Users:
    Click here to access the software
    You cannot save your data in ArrayTrack™, but you can use the analysis and interpretation tools to access the data that is stored on your local computer.
    Learn more in the ArrayTrack™ Quick Help Manual.
  • Private Account Support:
    Non-FDA users who want to deposit their data in the FDA/NCTR database, please e-mail us at NCTRBioinformaticsSupport@fda.gov to request a user account and password, and then click here to access the software.
  • Locally Installed Version:
    Non-FDA users who do not want to deposit your data in the FDA/NCTR database, you can request that the entire ArrayTrack™ application be installed locally in your institute for managing your own data. For more information, please e-mail us at NCTRBioinformaticsSupport@fda.hhs.gov.

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What is ArrayTrack™’s system architecture?

ArrayTrack™ is a client-server system. The back-end (server) is an ORACLE relational database which manages the data and the front-end (client) application is developed using JAVA.

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What are the system requirements to access ArrayTrack™?

ArrayTrack™ uses machine-independent technology. Most users access ArrayTrack™ through a Web browser. Get information on the system requirements for the locally installed version.

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I am a new ArrayTrack™ user. What resources are available online to help me learn how to use ArrayTrack™?

An ArrayTrack™ Quick Help Manual is available and provides a quick overview of ArrayTrack™'s basic functionalities. For more instructions, several detailed tutorials are also available online.

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How long will it take to download ArrayTrack™?

You will notice some delay the first time you run ArrayTrack™ because the entire ArrayTrack™ application must be downloaded. You may need to update your version of Java before ArrayTrack™ itself is started. Future uses of the software will only download parts of the application that have been changed, if any, and should start much quicker.

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What does this error message mean? “Connection failed: the network adapter could not establish the connection"

This might be due to your organization's firewall. Many firewalls are set up to only allow traffic to destination port 80 on remote hosts (Web traffic). However, the ArrayTrack™ server needs to be contacted on port 1610. Thus, you need to contact your system administrator about this particular port number (port 1610) that may need to be opened as an allowed destination port for outgoing connections on your organization's firewall. The following statement is prepared for your convenience to communicate with your system administrator: "The ArrayTrack™ server is listening on port 1610 for connections from the ArrayTrack™ client software. An organization whose hosts are to run the ArrayTrack™ client software needs to allow outgoing connections from any port (source port is randomly chosen on the client as is usual with Internet communications), to the fixed destination port of 1610 on.”

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What does this error message I received during installation mean? “Couldn’t load jnlp file to …."

Follow the steps below to fix the problem:

  • Open the "Tools" menu of your Internet browser and select "Internet Options.
  • Select the "General" tab and click the "Settings" button in the "Temporary Internet Files" section.
  • Select the "Every visit to the page" radio button.
  • Click "OK."
    Note: If you still receive the error message after following the steps above, repeat Steps 1 and 2, click the "Delete Files" button instead of the "Settings" button in Step 2 and click "OK."

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How do you contact the ArrayTrack™ team (to report bugs, recommend new functions…)?

Please e-mail NCTRBioinformaticsSupport@fda.hhs.gov if you have any suggestions to improve the software, report bugs, or implement new analysis functions.

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How do you open the Java console in order to allow for the diagnosis of any ArrayTrack™ problems?

  1. Click the Windows "Start" button and select "Control Panel" from the list.
  2. Click the "Java" icon to open the Java Control Panel.
  3. Click the "Advanced" tab and then click "Java console."
  4. Click on the "Show console" radio button and then click "OK."
  5. Restart ArrayTrack™. The Java console will be open every time you start ArrayTrack™. Keep it open at all times. 

If you encounter a problem, please check the Java console, copy the error message, and e-mail it to NCTRBioinformaticsSupport@fda.hhs.gov.

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What does this error message mean, "Unable to launch ArrayTrack™"?

This error message is usually a result of using an older version of Java (1.4 or previous). Please install a newer version of Javadisclaimer icon.

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How can I remove the locally installed non-prompted version of ArrayTrack™ from my computer?

First, remove the preferences file which is usually found under C:\Document and Settings\<you>\ArrayTrack™\ because it contains sensitive log-in information. It is not necessary to proceed further unless you would like to free up space being used by the cached application code file. To do this:

  1. Click the Windows "Start" button and select "Control Panel" from the list.
  2. Click the "Java" icon to open the Java Control Panel.
  3. Click the "View" button on the "General" tab.
  4. Select ArrayTrack™ (local database) and click the red "X" to remove the file.

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What are the security levels available in ArrayTrack™?

When installing ArrayTrack™ locally, several security levels are available.

  • ArrayTrack™-Level Security (Available in all ArrayTrack™ versions.)
    Under this security level, only the owner of the experiment can grant permissions to other users. Five different privileges are available to provide user-specific security levels for individual experiments.
  1. Read: Users assigned this privilege can view or export the dataset. They can also perform analyses on the dataset.
  2. Create Gene Lists: Users assigned this privilege have the same privileges as 1 above, and can also create and save gene lists within the experiment.
  3. Normalize: Users assigned this privilege have the same privileges as 1 above, and also the ability to normalize the data.
  4. Write: Users assigned this privilege have the same privileges as 1-3, can make changes to the experiment, and can delete the experiment if necessary.
  5. Manage Permissions: Users holding this privilege for an experiment can grant and revoke data permissions from other users for that particular experiment. However, this user does not implicitly have the permissions mentioned above in 1-4. The owner of an experiment, when importing array data, will be given privileges to write and manage permissions.
  • Operating System-Level Security (Availablein the unprompted local version used at NCTR.)
    View ArrayTrack™ installation instructions for unprompted log-in setup.
    This is the simplest option. For trusted users on trusted networks only. Security is applied by the ArrayTrack™ application itself based on the OS-reported user ID. Get more information about ArrayTrack™ security levels.
  • Oracle Database-Level Security (Available in the prompted local version.)
    View ArrayTrack™ installation instructions for prompted log-in setup.
    This version is more secure than the unprompted version and can be made very secure with the help of an active database administrator. This option provides an additional level of security. The Oracle Database Administrator (DBA) manages all the security functions and only the DBA can allow users to access data in ArrayTrack™. However, having to obtain permissions from the DBA may be of some inconvenience to users. This option, therefore, is more secure but is also more restrictive. Only users who require high security for their data use this option. Get more information about ArrayTrack™ security levels.

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What does this error message mean, "Error processing Cell files with R" that arises when performing probe-set conversion?

This is an R/Bioconductor-generated error that occurs when the memory in the user’s computer is not sufficient to run the R-probe set conversion. Possible solutions include:

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Can ArrayTrack™ be run on Linux systems?

Yes, Linux is supported. However, manual setup of R/Bioconductor is necessary for performing probe-set conversion and SAM analysis. For setup information, please refer to the R/Bioconductor installation instructions for Linux/Unix systems.

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Is installation of the R server required for performing Affymetrix probe set summarization or SAM analysis?

No, the installation of R/Bionconductor on the Windows platform is completely automated within the ArrayTrack™ application. R server installation is not needed. However, it may be beneficial to install an R server in order to handle memory-intensive analysis on large datasets. For more information, please refer to the Local R-server installation instructions.

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How will importing microarray data into ArrayTrack™ affect the space increase in the local Oracle database?

The microarray data files vary in size based on the array types and the format of the data file. A data file in .txt format will only occupy a small amount of space in the Oracle database as compared to at the OS level. But if you choose to perform further normalization of this imported .txt file, you need to remember that the normalized data will also occupy space in the database.

Affymetrix data is a little different. When Affymetrix data is saved to the database, ArrayTrack™ not only saves the original cell files as BLOB type, but also saves the converted cel files if the user applies MAS5 (default), RMA, Plier, DChip, etc. It parses the data files into individual records and stores them in the RAW intensity table. If the data is normalized then it is also stored separately. There are indexes that will occupy space as well. So the space required in the ArrayTrack™ database to store all this information about an Affymetrix data file will be significantly (about four times) bigger than the actual size of the cel file itself at the OS level.

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Can the database run on a SQL server database?

No, it can only run on an Oracle database server. However, this feature may become available in later versions of ArrayTrack™.

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How can I import a dataset where expression values for several hybridizations are saved in a single spreadsheet file?

In order to import raw data into ArrayTrack™, each hybridization needs to be saved in separate files, i.e. one file for each hybridization. However, some users may have a single spreadsheet file with data about all the hybridizations. For example, expression data for 10 hybridizations could be saved in one spreadsheet file. In such a situation, users need to split the spreadsheet file into multiple files first before importing into ArrayTrack™. ArrayTrack™ provides a function for users to easily split files. Please see ArrayTrack™ Tutorial 10: Other Useful Functions and Tutorial 9A: Data Import.

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What does this error message mean, "Could not create the Java virtual machine" when trying to start ArrayTrack™?

This problem is likely due to the Java Runtime Environment (JRE) that you have installed on your system. If you have the most recent version (JRE 1.6.0_18), try uninstalling and reinstalling a slightly older version, available here.

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Can ArrayTrack™ be run on Mac OS X systems?

Yes, Mac OS X is supported. However, you must install R and the Biocunductor packages manually in order to perform probe-set conversions or SAM analysis. For setup information please refer to the R/Bioconductor installation instructions for Mac OS X systems.

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How can I obtain a copy of ArrayTrack™ to install and administer locally?

While we maintain a centrally installed ArrayTrack™ database and are able to provide accounts to non-FDA users wishing to store their microarray data, we understand that both for convenience and data security and privacy reasons some groups of users may wish to install and administer their own local version of an ArrayTrack™ database. To obtain a DVD with the scripts and data necessary for a local installation please contact us at NCTRBioinformaticsSupport@fda.gov. Please also see "What are the requirements for running a locally installed version of ArrayTrack™?" for more information on system requirements.

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What are the requirements for running a locally installed version of ArrayTrack™?

To run a locally installed version of ArrayTrack™ you must have a license for Oracle Standard Edition or Oracle Enterprise Edition Version 10g or above. It is also highly recommended that a qualified database administrator perform the installation and configuration of the Oracle database, run the included scripts to create the ArrayTrack™ schemas and import necessary data, and perform any upgrades to the ArrayTrack™ database that may be released. Specific system requirements for installing and running ArrayTrack™ locally can be found in page "ArrayTrack™ Local Installation System Requirements".

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Why is there no reponse when "Install ArrayTrack" is clicked and what do I do?

The link to start the installation of the application needs Java Web Start enabled in your web browser. In some web browsers (Mozilla Firefox, Google Chrome, etc.) or operating systems (MS Windows 7, Mac OS X, etc.), the Java Web Start may not correctly link to the ArrayTrack™ launcher. The work-around is to manually open the ArrayTrack™ launcher. To do so, right click the link "Install ArrayTrack" from the web page, select "Save Link As ..." from the pop-up menu, then save the launcher file to your local hard drive. Find the downloaded launcher file, "arraytrack_extusr_bs.jnlp", on the drive, and try one of the following approaches to launch it:

  • Double-click the file name to start with Java Web Start.
  • Right-click the file name then select "Launch" from the pop-up menu.
  • Right-click the file name and select "Open With" from the pop-up menu, and select the application "Java Web Start" to run the launcher.
     

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Contact Information

Collaboration Information:Dr. Weida Tong (870-543-7142 or weida.tong@fda.hhs.gov)
Assistance Using ArrayTrack™:Feng Qian (870-543-7290 or feng.qian@fda.hhs.gov)
Submit Suggestions:Dr. Hong Fang (870-543-7538 or hong.fang@fda.hhs.gov)
Report Technical Problems:NCTRBioinformaticsSupport@fda.hhs.gov
 


ArrayTrack™ is a product designed and produced by the National Center for Toxicological Research (NCTR). FDA and NCTR retain ownership of this product. 
© Copyright 2004-2013, NCTR/FDA.


 

 

Contact FDA

870-543-7000
National Center for Toxicological Research

Food and Drug Administration

3900 NCTR Road

Jefferson, AR 72079