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h2. caArray Community Contribution

* [caArray 054 - Step-By-Step Guide to Install and Use caArray Importer|caArray 054 - Step-By-Step Guide to Install and Use caArray

 Importer]
* [caArray 080 - A Step-by-Step Guide to Create a MAGE-TAB Template Specific to RPLA Project|caArray 080 - A Step-by-Step Guide to Create a MAGE-TAB Template Specific to RPLA

 Project]

h2. caArray Installation and Upgrade

* [caArray 005 - Do I need to create an empty database prior to caArray or other LSD tool installations?|caArray 005 - Creating an empty database prior to caArray or other LSD tool installations]
* [caArray 006 - Step by Step Guide to Install caArray 2.x Grid Service (caArray 2.2 and Under)|caArray 006 - Step by Step Guide to Install caArray 2.x Grid Service (caArray 2.2 and Under)]
* [caArray 015 - How do I solve caArray 2.2.0\+ problems with localhost and related issues?|caArray 015 - Solving caArray 2.2.0-plus problems with localhost and related issues]
* [caArray 020 - How do I configure Eclipse for caArray?|caArray 020 - Configuring Eclipse for caArray]
* [caArray 026 - Can I change the port number after caArray installation?|caArray 026 - Changing the port number after caArray installation]
* [caArray 027 - How do we avoid a JBOSS port conflict between applications such as caArray and caTissue Suite?|caArray 027 - Avoiding a JBOSS port conflict between applications such as caArray and caTissue Suite]
* [caArray 028 - How do I point the caArray grid service to a different grid indexing service?|caArray 028 - Pointing the caArray grid service to a different grid indexing service]
* [caArray 030 - Which ports are required for caArray to run?|caArray 030 - Ports required for caArray to run]
* [caArray 031 - How do we install caArray on multiple servers?|caArray 031 - Installing caArray on multiple servers]
* [caArray 044 - Should my caArray grid service be Analytical or Data Service?|caArray 044 - caArray grid service - Analytical or Data Service]
* [caArray 057 - I deployed caArray in Eclipse but got exception when I tested the caArray. Why?|caArray 057 - caArray deployed in Eclipse - exception when caArray tested]
* [caArray 058 - Are there any guidelines for applying OS patching and Java updates on servers running caArray?|caArray 058 - Guidelines for applying OS patching and Java updates on servers running caArray]
* [caArray 059 - Where do I download the caArray 2.3.1 GUI Installer?|caArray 059 (DEPRECATED) - Download for the caArray 2.3.1 GUI Installer]
* [caArray 062 - Where to get a complete list of caArray service URLs?|caArray 062 - Complete list of caArray service URLs]
* [caArray 066 - The installation for caArray installation or upgrade failed. Where can I find the error log?|caArray 066 -  Installation for caArray installation or upgrade failed - finding the error log]
* [caArray 070 - An error reports the wrong version of Java. What is the problem?|caArray 070 - An error reports the wrong version of Java]
* [caArray 077 - How do we increase time-out period when running CQL queries?|caArray 077 - Increasing time-out period when running CQL queries]
* [caArray 079 - Are there secure Grid services for caArray?|caArray 079 - Secure Grid services for caArray not supported]
* [caArray 083 - Can we delete the legacy files during caArray upgrade?|caArray 083 - Deleting the legacy files during caArray upgrade]
* [caArray 078 - What browsers does caArray support?|caArray 078 - Browsers supported by caArray]
* [caArray 091 - Internet connection not needed for the caArray GUI installer|caArray 091 - Internet connection not needed for the caArray GUI installer]
* [caArray 093 - How To Build caArray From Source Code - An Illustrated Tutorial|caArray 093 - How To Build caArray From Source Code - An Illustrated Tutorial]

h2. Introduction to caArray Usage

* [caArray 049 - Introduction to caArray - a High-level Workflow|caArray 049 - Introduction to caArray - a High-level Workflow]
* [caArray 050 - Introduction to caArray - Browse and Search caArray Repository|caArray 050 - Introduction to caArray - Browse and Search caArray Repository]
* [caArray 095 - Lists of Must-Have and Nice-to-Have Features to Support Next-Generation Sequencing Data|caArray2:caArray 095 - Lists of Must-Have and Nice-to-Have Features to Support Next-Generation Sequencing Data]


h2. caArray User Account, Login and Admin Issues

* [caArray 041 - caArray Account Management|caArray 041 - caArray Account Management]
* [caArray 029 - How do I change the caArray admin e-mail address after installation?|caArray 029 - Changing the caArray admin e-mail address after installation]
* [caArray 035 - How do we choose the correct caArray access role for a user?|caArray 035 - Choosing the correct caArray access role for a user]
* [caArray 065 - Can we amend the ownership for a deleted user's experiment?|caArray 065 - Amending the ownership for a deleted user's experiment]
* [caArray 084 - Can users change their passwords in caArray?|caArray 084 - Changing user passwords in caArray]
* [caArray 024 - Does the caArray user account with system administrator role have access to all experimental data?|caArray 024 - Access for caArray user account with system administrator role  to all experimental data]
* [caArray 045 - User registration is unable to send the user an email to confirm registration. What do we do?|caArray 045 - User registration is unable to send the user an email to confirm registration]

h2. Working with Array Design Files

* [caArray 039 - Array Design Files|caArray 039 - Array Design Files]
* [caArray 036 - Working with Array Design Files in caArray|caArray 036 - Working with Array Design Files in caArray]
* [caArray 010 - Where are the Array Design Files for caArray?|caArray 010 - Location of the Array Design Files for caArray]
* [caArray 052 - I would like to download an array design file, but I can't find it in caArray. Why?|caArray 052 - Cannot find an array design file in caArray]
* [caArray 074 - Can I rename a design file and use it in a study?|caArray 074 - Renaming a design file and using it in a study]
* [caArray2:caArray 094 - Handling Array Designs]
* caArrayDemo-004 [Using caArray: Uploading Array Design File|caArray Demos^Array-design-file.ppt]

h2. Working with MAGE-TAB Files

* [caArray 037 - MAGE-TAB Files|caArray 037 - MAGE-TAB Files]
* [caArray 007 - What are MAGE-TAB Files?|caArray 007 - MAGE-TAB Files]
* [caArray 008 - Should I use the Annotations tab or MAGE-TAB annotation files to annotate my experiment?|caArray 008 - Using the Annotations tab or MAGE-TAB annotation files to annotate an experiment]
* [caArray 009 - Highlights for Building caArray's MAGE-TAB Annotation Files|caArray 009 - Highlights for Building caArray's MAGE-TAB Annotation Files]
* [caArray 060 - How do I export experiment annotation and data file into MAGE-TAB and GEO SOFT formats?|caArray 060 - Exporting experiment annotation and data file into MAGE-TAB and GEO SOFT formats]
* [caArray 080 - A Step-by-Step Guide to Create a MAGE-TAB Template Specific to RPLA Project|caArray 080 - A Step-by-Step Guide to Create a MAGE-TAB Template Specific to RPLA Project]
* caArrayDemo-001 [How to load MAGE-TAB data into caArray|caArray Demos^CaArray_Demo_MAGE-TAB_Data_Upload_4_Revised_2.wmv]

h2. Working with Data Files

* [caArray 019 - caArray File Loading Process|caArray 019 - caArray File Loading Process]
* [caArray 002 - How do I upload MicroArray Gene Expression Data into caArray?|caArray 002 - Uploading MicroArray Gene Expression Data into caArray]
* [caArray 013 - Is there any size or format limitation on the files uploaded to caArray?|caArray 013 - Size or format limitation on the files uploaded to caArray]
* [caArray 014 - Which files can be uploaded into caArray?|caArray 014 - Files that can be uploaded into caArray]
* [caArray 016 - Which file can be parsed into caArray? What is the benefit of file parsing?|caArray 016 - File Parsing into caArray]
* [caArray 092 - Importing Data into caArray|caArray 092 - Importing Data into caArray]
* [caArray 017 - What is the meaning of the caArray Status of Importing - Imported versus Imported Not Parsed?|caArray 017 - Meaning of the caArray Status of Importing - Imported versus Imported Not Parsed]
* [caArray 018 - What causes the error "Failed Validation"?|caArray 018 - Cause of the error Failed Validation]
* [caArray 051 - Which columns in Illumina expression csv array design files are acceptable in caArray?|caArray 051 - Columns in Illumina expression csv array design files acceptable in caArray]
* [caArray 056 - How do I import an Affy .TXT file into caArray?|caArray 056 - Importing an Affy .TXT file into caArray]
* [caArray 061 - What is the difference between the annotation options that are available when importing data?|caArray 061 - Difference between the annotation options that are available when importing data]
* [caArray 067 - How do I resolve an error with unpacking the zip files?|caArray 067 - Resolving an error with unpacking the zip files]
* [caArray 076 - How can I upload and store QC data in caArray?|caArray 076 - Uploading and storing QC data in caArray]
* [caArray 082 - The datafile is imported, but it is not downloadable. Why?|caArray 082 - Datafile imported but not downloadable]
* [caArray 023 - Can multiple users upload microarray datafiles under the same experiment?|caArray 023 - Upload of microarray datafiles by multiple users under the same experiment]
* [caArray 025 - Does caArray have version control on uploaded files?|caArray 025 - caArray version control on uploaded files not supported]
* [caArray 087 - Why Do I Get an Error Message When Attempting to Validate an Illumina SNP Data File in caArray?|caArray 087 - Error Message When Attempting to Validate an Illumina SNP Data File in caArray]
* [caArray 089 - How Do I Upload Very Large Datasets?|caArray 089 - Uploading Very Large Datasets]

h2. Managing Experiments

* [caArray 088 - Finding Information on an Experiment|caArray2:caArray 088 - Finding Information on an Experiment]
* [caArray 038 - caArray Experiment Management|caArray 038 - caArray Experiment Management]
* [caArray 034 - Can I edit my experiment that has already been made public?|caArray 034 - Editing an experiment that has already been made public]
* [caArray 012 - How do I add an organism to the Organism List in caArray?|caArray 012 - Adding an organism to the Organism List in caArray]
* [caArray 032 - Can I recover a mistakenly deleted experiment from a caArray database backup?|caArray 032 - Recovering a mistakenly deleted experiment from a caArray database backup]
* [caArray 072 - Can I delete an experiment with the status as "In Progress"?|caArray 072 - Deleting an experiment with the status as In Progress]
* [caArray 090 - How do I change the inactivity session timeout delay?|caArray 090 - Changing the inactivity session timeout delay]

h3. Administrative Tasks in caArray

* [caArray 077 - How do we increase time-out period when running CQL queries?|caArray 077 - Increasing time-out period when running CQL queries]
* [caArray 100 - caArray Audit Trails|caArray 100 - caArray Audit Trails]
* [caArray 068 - What can we find in an audit file?|caArray 068 - Contents of an audit file]

h3. Experiment Visibility and Data Sharing

* [caArray 043 - Manage the Public Visibility of a caArray Experiment|caArray 043 - Manage the Public Visibility of a caArray Experiment]
* [caArray 071 - How do I check if I am actually on caGrid sharing my microarray data?|caArray 071 - Checking if I am actually on caGrid sharing my microarray data]
* [caArray 046 - Management Account Ownership|caArray 046 - Management Account Ownership]
* [caArray 022 - Can I change the ownership of the experiment in caArray?|caArray 022 - Changing the ownership of the experiment in caArray]
* [caArray 040 - caArray Global Settings|caArray 040 - caArray Global Settings]
* caArrayDemo-002 [How to Use caArray to Share Pre-Publishing Data?|caArray Demos^Sharing_Prepublished_data.ppt]

h2. caArray Integration with Other Applications

h3. caArray and UPT Integration

* [caArray 047 - How do I create a caArray account with UPT?|caArray 047 - Creating a caArray account with UPT]
* [caArray 001 - Is UPT required for caArray or other application tools in LSD Bundle?|caArray 001 - UPT required for caArray or other application tools in LSD Bundle]
* [caArray 003 - How do I create a caArray user with UPT?|caArray 003 - Creating a caArray user with UPT]
* [caArray 011 - What do I do when I see the error "Invalid Login" or the "No Application found" error when I log in via UPT"?|caArray 011 - Invalid Login or No Application found error when logging in via UPT]
* [caArray 086 - UPT was installed successfully but I could not log in as the super user to set up caArray. Why?|caArray 086 - UPT installed successfully but could not log in as the super user to set up caArray]
* [caArray 053 - How do I remove the lock on my UPT superuser account?|caArray 053 - Removing the lock on my UPT superuser account]
* [caArray 021 - How to I configure caArray for LDAP authentication?|caArray 021 - Configuring caArray for LDAP authentication]
* caArrayDemo-005 [Using UPT: Set up Application & Create caArray Users|caArray Demos^CaArray-UPT.ppt]
* [caArray 042 - Is "user password" a required field for new user creation in UPT?|caArray 042 - User password field in new user creation in UPT]
* [caArray 075 - What is the difference between the "Group" in the UPT and the "Collaboration Group" in caArray?|caArray 075 - Difference between the Group in the UPT and the Collaboration Group in caArray]
* [caArray 086 - UPT was installed successfully but I could not log in as the super user to set up caArray. Why?|caArray 086 - UPT installed successfully but could not log in as the super user to set up caArray]

h3. caArray and geWorkbench Integration

* [caArray 004 - Can I access the geWorkbench application from caArray?|caArray 004 - Access to the geWorkbench application from caArray]
* [caArray 033 - What is the version compatibility between geWorkbench and caArray?|caArray 033 - Version compatibility between geWorkbench and caArray]
* caArrayDemo-003 - [Using geWorkbench to Remote Access caArray Data|caArray Demos^GeWorkbench_Remote_Access.ppt]

h3. caArray and caIntegrator Integration

* [caArray 081 - Can caArray and caIntegrator2 share the same version of the UPT application?|caArray 081 - caArray and caIntegrator2 sharing the same version of the UPT application]

h3. caArray and caTissue Integration

No FAQ at this time.

h2. For more information

Still can not find the answer to your questions? Please try one of following online resources:

[caGrid Trouble Shooting|http://www.cagrid.org/wiki/CaGrid:How-To:TroubleshootIndexService]










[UPT and CSM FAQs|https://wiki.nci.nih.gov/x/ygGy]










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