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ArrayTrack™ Frequently Asked Questions

Q1: What is ArrayTrack™?

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

a) a database (MicroarrayDB) that stores microarray data and associated toxicological information;

b) tools (TOOL) for data visualization and analysis; and

c) libraries (LIB) that provide curated functional data from public databases for data interpretation.

Using ArrayTrack™, we 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. (more on ArrayTrack™)

Q2: What microarray data can be stored in ArrayTrack™?

• ArrayTrack™ handles both two channels 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).

Q3: 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 Benjamini-Hochberg method, principal component analysis (PCA), hierarchical clustering analysis (HCA) and etc.

Q4: How can ArrayTrack™ enhance the interpretation of microarray results?

• ArrayTrack™ contains a rich collection of information on gene annotation. It is straightforward to obtain functional information such as chromosomal locations, GO terms, pathways, summary, references for a gene. For genes being analyzed, ArrayTrack™ also provides direct hyperlinks to public genome-related websites, including LocusLink, Unigene, GenBank, GeneCards, OMIM, GO, KEGG, and others.
• The emphasis 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 gene 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.

Q5: Who can access ArrayTrack™?

ArrayTrack™ is developed by the U.S. Food and Drug Administration (FDA) National Center for Toxicological Research (NCTR). Currently, ArrayTrack™ is freely available to both academic users and profit organizations. (please check here to find out how to access or obtain a copy of ArrayTrack™)

Q6: How to access ArrayTrack™?

• FDA users – Click here to access the software. You can upload the data and use the analysis and interpretation tools to make sense out of the data. (Note: your data will be stored in a database that is resided in NCTR)
• Non-FDA users - Click here to access the software. Till today, we do not support public data deposition. You cannot save the data in ArrayTrack™, but you can use the analysis and interpretation tools to access the data that is stored in your local PC (the details for using this mechanism is available in the ArrayTrack™ manual).
• Private account support – For non-FDA users who want to deposit the data in the FDA/NCTR database, please contact us to request a user account and password, and then click here to access the software.
• Locally installed version – If you select one of the three aforementioned ways to access ArrayTrack™, your data is stored in our database (at the FDA/NCTR). However, you can request an entire ArrayTrack™ application to be installed locally in your institute for managing your own data.   Please contact us.

Q7: What is ArrayTrack™’s system architecture?

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

Q8: What are the system requirements to access ArrayTrack™?

ArrayTrack™ uses machine-independent technology. Most users access ArrayTrack™ through a web browser. Information on the system requirements for the locally installed version is available here.

Q9: Is data secured in ArrayTrack™?

ArrayTrack™ has a data ownership control (security) function. The owner of the data assigns the “read and/or write” authority to colleagues/collaborators at the individual experiment level.

Q10: How long will take to download ArrayTrack™?

You will notice some delay the first time you run ArrayTrack™ due to the need to download the entire ArrayTrack™ application. You may also be prompted 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.

Q11: What is this error message “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.”

Q12: What is this error message during installation “Couldn’t load jnlp file to ….?"

The following steps will fix the problem:

1. open “Internet Options…” under the “Tools” menu of our or any website;
2. select the “General” Panel and click the “Settings…” button in the Temporary Internet files section (2nd section); and
3. select the “Every visit to the page” check box, and click OK. If it still doesn’t fix the problem, click the “Delete Files” button instead of the “Settings…” button in Step 2 and click OK.

Q13: How do you contact ArrayTrack™ team (to report bugs, recommend new functions…)?

Please contact us if you have any suggestions to improve the software, report bugs or implement new analysis functions.

Q14: How do you open the Java console in order to allow for the diagnosis of any ArrayTrack™ problems?

1. Go to the Windows Start button, then select Control Panel

2. Click the Java icon to open the Java Control Panel.

3. Click the Advanced tab.

4. Check Show console under Java console.

5. Restart ArrayTrack™. The Java console will be open every time you start ArrayTrack™. Keep it open at all times. When you encounter problem, please check the Java console and copy the error message to us. This will help us to diagnose the problem.

Q15: What is this error message "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 Java from http://www.java.com/en/download/index.jsp

Q16: How can the locally installed non-prompted version of ArrayTrack™ be removed from the computer?

First, remove the preferences file which is usually found under C:\Document and Settings\<you>\ArrayTrack\ because it contains sensitive login information. It is not necessary to proceed further unless you would like to free up space being used by the cached application code file.  In order to do this, go to Control Panel ->Java->Temporary Internet files, click the View button, then select “ArrayTrack™ (Local Database)” and click the button marked X to remove the file.

Q17: What are the security levels available in ArrayTrack™?

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

A. Security at ArrayTrack™ level (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, in addition to viewing, exporting and performing analyses (1), can also create and save gene lists within the experiment.
3. Normalize: Users assigned this privilege have the ability to normalize the data in addition to viewing, exporting and performing analyses (1) on it.
4. Write: Users assigned this privilege can do all the above (1-3) and in addition, can make changes to the experiment and can delete the experiment if need be.
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 (1-4).

The owner of an experiment, when importing array data, will be given privileges to write and manage permissions.

B. Security at operating system level - unprompted local version used in NCTR/FDA. (See ArrayTrack™ installation instructions for unprompted login 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. (See ArrayTrack™ Security Levels- Detailed Information for more information)

C. Security at Oracle database level - prompted local version (See ArrayTrack™ installation instructions for prompted login 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 DBA (Database administrator) manages all the security functions and only he 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. (See ArrayTrack™ Security Levels- Detailed Information for more information)

Q18: What is this error message "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. In such a case some solutions could be installing an R server, using a Linux client or increasing the memory capacity of the computer running the analysis.

Q19: Can ArrayTrack™ be run on Linux systems?

Yes, Linux is supported. But, 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.

Q20: 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.

Q21: I am a new ArrayTrack™ user. What resources are available online to help me learn how to use ArrayTrack™?

A quick start manual is available and provides a quick overview of the basic ArrayTrack™ functionalities. For more instructions, several detailed tutorials are also available online.