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Agilent Feature Extraction 12.1 Microarray Installation Guide PDF
Summary of Content for Agilent Feature Extraction 12.1 Microarray Installation Guide PDF
Agilent Feature Extraction 12.1
Installation Guide
For Research Use Only. Not for use in diagnostic procedures.
Quick Start Installation of Agilent Feature Extraction 12.1 2
Flow chart for installation 3
Instructions for Installing Agilent Feature Extraction 12.1 4
Removing the Feature Extraction and QC Chart Tool Software 22
Getting Help 25
To get help within Agilent Feature Extraction 12.1 25
To contact Agilent Technical Support 26
This guide explains how to install Agilent Feature Extraction 12.1 software for standalone use. This software is compatible with Agilent Genomic Workbench Lite Edition. Agilent Feature Extraction 12.1 can be installed on a computer with Agilent CytoGenomics 2.5 or later or GeneSpring 12.0 or 12.5 installed. Do not install Feature Extraction 12.1 on a computer with Feature Extraction 11.0, 11.5, or 12.0 until that previous version has been uninstalled.
Agilent Technologies
Quick Start Installation of Agilent Feature Extraction 12.1
Feature Extraction 12.1 is installed by running the installation program and following the installation wizard steps, described in this guide. When you run the installation program, both Feature Extraction and QC Chart Tool are installed.
If you have the following software installed on your computer, you can install Feature Extraction 12.1:
Feature Extraction 10.7 or earlier standalone version
Agilent CytoGenomics 2.5 or later
Agilent Genomic Workbench Lite edition
GeneSpring 12.0 or 12.5
NOTE If Feature Extraction 11.0, 11.5, or 12.0 is installed on the computer, do not install Feature
Extraction 12.1 until you uninstall the previous version. If Feature Extraction 11.5 or 12.0 is
installed, you can use the Migration Utility program for Feature Extraction 12.1 to export
grid templates, protocols, and QC metric sets prior to uninstallation. You can then use the
Migration Utility program to import these files into Feature Extraction 12.1. See the
Migration Utility Guide for detailed instructions.
2 Agilent Feature Extraction Installation Guide
Flow chart for installation
Make sure the person installing the software has full administrator permissions on the installation computer. See d. Set up permissions for installer on page 7.
Download the installation package from the Agilent website. See a. Download the software and release notes on page 4.
Step 1. Prepare for installation.
Make sure that the computer meets system specifications. See b. Check system requirements before you start on page 5.
Use Control Panel to adjust User Account Control settings. See e. Adjust User Account Control settings on page 7.
If you have a previous version of Feature Extraction standalone installed on your computer, back up your data. See c. If you have a previous version installed, back up data on page 6.
If Feature Extraction 11.5 or 12.0 is already installed on the computer, you cannot install Feature Extraction 12.1 until you uninstall the previous version. Before uninstalling, use the Migration Utility program to export grid templates, protocols, and QC metrics that can later be imported into Feature Extraction 12.1.
Step 2. Install the Feature Extraction software.
Step 3. Add your software license.
Step 4. Start the Feature Extraction program.
Agilent Feature Extraction Installation Guide 3
Instructions for Installing Agilent Feature Extraction 12.1
This section includes more detailed instructions and important notes about each step of the installation process. These steps are outlined in the installation flow chart shown in Flow chart for installation on page 3.
Upgrade from previous versions is not supported. Use the steps in this section to install
Feature Extraction 12.1.
Step 1. Prepare for installation
a. Download the software and release notes
1 Go to the Feature Extraction product page on the Agilent website: www.agilent.com/en/product/mirna- microarray- platform/mirna- micro array- software/feature- extraction- software- 228496.
2 Click Downloads to open the Download Software Feature Extraction Software page.
3 Click Download.
4 Click Save File to save the Feature Extraction installation package zip folder to your computer. (Depending on your internet connection speed, the download can take a long time.)
The zip folder contains the Agilent Feature Extraction 12.1 installer, the Microsoft Visual C++ 2008 Redistributable Package installer (vcredist_x86.exe), the Agilent Feature Extraction 12.1 Installation Guide PDF, and the Agilent Feature Extraction 12.1 Release Notes PDF.
5 At completion of the download, open the zip folder and decompress the contents.
NOTE
NOTE You only need to install the Microsoft Visual C++ Redistribution Package if you will be
installing Feature Extraction on a PC that, 1) was not provided by Agilent, and 2) is running
Windows 10 version 1803 or later.
4 Agilent Feature Extraction Installation Guide
b. Check system requirements before you start
Check to make sure that your computer system meets the following requirements. If necessary, install any required software programs that are needed to support Agilent Feature Extraction 12.1.
If an operating system is not listed, it is not supported.
Table 1 Minimum Requirements for Agilent Feature Extraction computers
Computer requirements for Windows
Operating system
* An installer for the Microsoft Visual C++ Redistribution Package (vcredist_x86.exe) is included in the Feature Extraction
installation package zip folder that you downloaded from the Feature Extraction Software Download page of the Agilent
website. You only need to install the Microsoft Visual C++ Redistribution Package if you will be installing Feature Extraction on
a PC that, 1) was not provided by Agilent, and 2) is running Windows 10 version 1803 or later. If installation of the Microsoft
Visual C++ Redistribution Package is required for your system, install it prior to installing Feature Extraction by launching the
vcredist_x86.exe file. Then, restart your system and install Feature Extraction.
NOTE
Windows 7, 64-bit:
Professional SP1
Enterprise
Windows 10, 64-bit:
Pro
Enterprise
Microsoft .NET framework Version 3.5
Microsoft .NET framework 3.5 is installed by default on machines running the
Windows 7 operating system. However, if you are running Windows 10, a user
with Administrator privileges will need to download and install Microsoft .NET
framework 3.5 before you install Feature Extraction.
Software Runtime components of Microsoft Visual C++ 2008*
Any software that enables you to open PDF files (for example, Adobe Reader)
Internet Explorer version 7 or later
Processor 2GHz or higher
Working memory (RAM) 4 GB or higher
Hard disk space 40 GB available
Display Resolution 1280 x768 or higher
Agilent Feature Extraction Installation Guide 5
c. If you have a previous version installed, back up data
If you have a standalone version of Feature Extraction 11.0, 11.5, or 12.0, back up your data and uninstall the previous version before installing Feature Extraction 12.1.
If you plan to remove the older version and/or transfer the data to the new version, do the following:
Export any user- created FE protocols and QC metric sets from the old version of Feature Extraction.
You can import or add the exported protocols and QC metric sets to the new database after you install Feature Extraction 12.1.
Export QC Chart Tool data.
To export data in your old QC Chart Tool database, use a QC Chart Tool query and then export the query results. You can then import this data to the newly installed QC Chart Tool database. Queries cannot be exported; recreate them in the new version of the software.
NOTE Feature Extraction version 12.1 does not support the manual import of grid template data
from Feature Extraction version 11.5 or 12.0. Use the Migration Utility program to transfer
grid templates from the previous version of Feature Extraction into Feature Extraction 12.1.
If you currently have Feature Extraction 11.5 or 12.0 installed, export all the data (grid
templates, protocols, and metric sets) from that version, and then uninstall Feature
Extraction before continuing. Once the previous version is uninstalled, you can install
Feature Extraction 12.1 and import the data that you exported from the previous version.
To download the Migration Utility program, go to
www.agilent.com/en/product/mirna-microarray-platform/mirna-microarray-software/fea
ture-extraction-software-228496 and click Downloads to open the Download Software Feature Extraction Software page. Then, click MIGRATION UTILITY TOOL.
CAUTION Do not use the Database Backup-Restore utility to back up the QC Chart Tool database. The
backup of the QC Chart Tool database using these methods cannot be loaded into the new
version.
6 Agilent Feature Extraction Installation Guide
d. Set up permissions for installer
Make sure that the user account used to install the Agilent Feature Extraction 12.1 software has administrator permissions on the installation computer.
The way you set permissions varies between operating systems. Contact your network administrator for help in checking or changing user account permissions. Administrator permissions are not required to run the Feature Extraction software.
e. Adjust User Account Control settings
Turn off the User Account Control before you install Feature Extraction 12.1. After you install the software, you can turn it on again.
Change the User Account Control settings from the default setting to Never Notify.
1 Go to Control Panel.
2 Click System and Security.
3 Click Change User Account Control setting (found under Action Center for Windows 7 and under Security and Maintenance for Windows 10).
4 Change the setting to Never Notify and click OK.
5 Restart the system.
Step 2. Install the Feature Extraction software The Agilent Feature Extraction 12.1 installation program installs the Agilent Feature Extraction, Agilent QC Chart Tool, and PostGreSQL software. After installation, the database server (PostGreSQL) runs silently in the background and manages the shared database for Agilent Feature Extraction 12.1 and QC Chart Tool.
1 Before installing Agilent Feature Extraction 12.1, complete all the preinstallation steps outlined in Step 1 of the Flow chart for installation on page 3.
2 Log on to the Windows system where you want to install Agilent Feature Extraction 12.1. Use an account that has administrator permissions.
Agilent Feature Extraction Installation Guide 7
3 Locate the installation program you downloaded in Step 1, a. Download the software and release notes on page 4. Double- click the installation program file to start the installation wizard.
The following message is displayed.
Figure 1 InstallAnywhere dialog box - preparing to install
The installation wizard starts.
Figure 2 Introduction screen for the installation wizard
8 Agilent Feature Extraction Installation Guide
4 Read the introductory information.
5 Click Next to display the next section.
The License screen appears.
Figure 3 License screen
6 Read the license agreement. Click I accept the terms of the License Agreement and then click Next. (Click Previous to review information in a previous section.)
The Choose Install Folder screen appears.
Agilent Feature Extraction Installation Guide 9
Figure 4 Choose Install Folder screen
7 By default, the software is installed in C:\Agilent\AgilentFeatureExtraction 12.1.X.X (where X.X is the revision number). Leave this folder, or type the path for the name of the folder where you want to install Agilent Feature Extraction 12.1.
For installations on Windows 7, the installation folder must not be in the C:\Program Files
folder.
OR
Click Choose, browse to a location where you want to install the software, and then click Save.
8 Click Next.
If there is a conflict in the port used to install PostGreSQL, the Get User Input screen appears. Otherwise, the Choose Shortcut Folder screen appears. See Figure 6 on page 12.
NOTE
10 Agilent Feature Extraction Installation Guide
Figure 5 Get User Input screen
9 Click Next.
The Choose Shortcut Folder screen appears.
NOTE If the default port 6002 is not available, you need to change the port number. Enter a new
port number that follows the same format, i.e., 600X, where X increments by one 1 until
the port is accepted (for example: 6003, 6004, etc.). Press Next to continue the installation.
The new port number entry will not be saved and must be updated manually by editing the
DBConnectinfo file found in the default Feature Extraction folder of your installation
folder: C:\Agilent\AgilentFeatureExtraction12.1.X.X\FeatureExtraction.
Agilent Feature Extraction Installation Guide 11
Figure 6 Choose Shortcut Folder screen
10 By default, program icons are installed in the AgilentFeatureExtraction 12.1.X.X program group on your computer (where X.X is the revision number). To select another location for the program icons, select the desired location (On the desktop, for example) and then click Next.
If more than one person plans to use Agilent Feature Extraction 12.1 on this computer,
select Create Icons for All Users. Otherwise, other users do not see the program icons.
The Warning screen appears.
NOTE
12 Agilent Feature Extraction Installation Guide
Figure 7 Warning screen
11 Read the message that cautions you not to stop the installation once it has started, and then click Next.
The Pre- Installation Summary screen appears.
Agilent Feature Extraction Installation Guide 13
Figure 8 Pre-Installation Summary screen
12 Review the installation setup information. If you want to change any of the settings, click Previous and go back and change the settings. To start the installation, click Install.
The Installing Agilent Feature Extraction 12.1.X.X screen appears and is displayed until the installation is complete.
14 Agilent Feature Extraction Installation Guide
Figure 9 Installing Agilent Feature Extraction 12.1.X.X screen
When the installation is complete, the Installation Complete screen is displayed.
13 Click Done.
Agilent Feature Extraction Installation Guide 15
Step 3. Add your software license
Types of licenses
Agilent supplies two kinds of licenses for Feature Extraction: demo and perpetual.
To install a demo license
If you want to try Feature Extraction before purchasing, you can download a 30- day demo license. The demo license expires 30 days from the date you download it. If you install the demo license on the same day that you downloaded it, Feature Extraction works for the next 30 days. However, if you wait until day 20 to install the downloaded demo license, the software only works for the remaining 10 days.
Follow the instructions to demo the software before purchase.
1 Go to: www.agilent.com/en/product/mirna- microarray- platform/mirna- microarr ay- software/feature- extraction- software- 228496 and click Downloads to open the Download Software Feature Extraction Software page.
2 Locate the statement about downloading a 30- day demo license. Click the link within this statement (on the word Download).
The License Request page opens.
3 Complete the form and click Submit Request.
Agilent processes the request and sends you a license key. You can continue installing the software without the license key, but you will need the license key in order to run the Feature Extraction.
4 Unzip the 30- day trial license file into the Feature Extraction installation folder.
Or, you can place the license anywhere you want. However, if the license file is not located in the installation folder, the following message appears when you start Feature Extraction.
NOTE The PDF QC reports are not available with the demo license. To get PDF QC reports, buy and
install a perpetual license.
16 Agilent Feature Extraction Installation Guide
Figure 10 License message
a Click Retry.
The following dialog opens.
Figure 11 Select Agilent Feature Extraction License File dialog box
b Find the folder that contains the unzipped license file.
c Select the license file (.lic), and click Open.
5 (Optional) To view when your demo license expires, from the Feature Extraction menu bar, click Help > About.
Agilent Feature Extraction Installation Guide 17
Figure 12 Current License Information - Demo
To install a perpetual license (with or without an Agilent scanner)
When you purchase Feature Extraction software, Agilent provides you with a perpetual license.
Perpetual license never expires.
Perpetual license is good for the current software version released at time of purchase.
Perpetual license is good toward new software versions released within the license term (1- year, 2- year, and 3- year licenses are available).
Instructions to set up a valid license depend on several situations:
If you want to try the software first before you purchase
If you have purchased a new version or an upgrade
If your license is about to expire or has expired, or is invalid
Because the Feature Extraction license uses the Ethernet MAC address as host ID,
the license becomes invalid if you remove or change Ethernet cards.
When you purchase Agilent Feature Extraction software, you receive a Software Entitlement Certificate (SEC). To redeem your purchased license, go to the Agilent Software License Redemption website and use the information on the certificate.
These instructions assume that you have already installed the software.
1 Start Feature Extraction. If Figure 10 appears, click Cancel.
2 Select Help > Agilent License. The internet browser opens to the Agilent Software License Redemption website at https://agilent.subscribenet.com.
Have the following items available:
CAUTION
18 Agilent Feature Extraction Installation Guide
Software Entitlement Certificate (SEC) - This PDF contains the Order Number and Certificate Number that you provide to redeem your purchased license.
Host ID - The Host ID can be found under the menu Help > About. You provide the host ID to redeem your purchased license.
3 Follow the instructions on the Agilent Software License Redemption website to redeem your license.
After redeeming the license on line, you will receive an email with the license attached.
4 Save the license file to your installation folder:
C:\Agilent\AgilentFeatureExtraction 12.1.X.X (where X is the revision number)
Or, you can place the license file anywhere you want. If the license file is not found in the installation folder when the program starts, it asks you to identify the location of the license file.
a If the Feature Extraction program is already running, open a project. Otherwise, double- click the Feature Extraction icon to open a project.
Figure 10, License message, on page 17 appears:
b Click Retry.
Figure 11, Select Agilent Feature Extraction License File dialog box, on page 17 appears.
c Find the directory that contains the license file.
d Select the license file (.lic), and click Open.
Feature Extraction opens automatically with FE_Project1.
5 (Optional) To view the date that your perpetual license is still good toward new software versions, click Help > About.
Figure 13 Current License Information - Perpetual
The date code displayed tells you what updates your license allows. For example, a date code of 2017.0730 indicates that the license is good towards new software versions released on or before July 30, 2017.
Agilent Feature Extraction Installation Guide 19
If your license expired, or is invalid for the software version
The software warns you 20 days before your license file expires. The following message appears.
Figure 14 License expiration message
Without a valid license you can still open an image, import templates and protocols, set up preferences and change protocols. You cannot open a project or open Grid Mode for manual gridding.
If you try to open a project in Feature Extraction and your license has expired or is not valid for the software version, an error message appears saying that your license expired or is invalid.
To acquire a valid Feature Extraction 12.1 license, contact Agilent Technologies.
1 Call your local sales representative or go online to: www.agilent.com/en/product/mirna- microarray- platform/mirna- microarr ay- software/feature- extraction- software- 228496 to purchase a new license.
After your purchase, you receive a Software Entitlement Certificate.
2 Start the Feature Extraction program and select Help > Agilent License.
Have the following items available:
Software Entitlement Certificate (SEC) - This PDF contains the Order Number and Certificate Number that you provide to redeem your purchased license.
Host ID - The Host ID can be found under the menu Help > About. You provide the Host ID to redeem your purchased license.
3 Follow the instructions on the Agilent Software License Redemption website to redeem your purchased license.
After redeeming the license on line, you will receive an email with the license attached.
20 Agilent Feature Extraction Installation Guide
4 Save the license file to the same path as your previous license.
You are now ready to work with Feature Extraction.
Step 4. Start the Feature Extraction program After you install the Agilent Feature Extraction software and license, start the program.
Double- click the Agilent Feature Extraction 12.1.X.X icon from your desktop or select Agilent Feature Extraction 12.1.X.X from the Windows Start menu.
How you start the program depends on the choice you made for Shortcut Folder during
installation of the Feature Extraction software.
To start the Agilent QC Chart Tool program
QC Chart Tool is a separate program that shares the database with Feature Extraction. To start the program,
Double- click the Agilent QC Chart Tool icon from your desktop or select Agilent QC Chart Tool from the Windows Start menu.
How you start the program depends on the choice you made for Shortcut Folder during
installation of the Feature Extraction software.
NOTE
NOTE
Agilent Feature Extraction Installation Guide 21
Removing the Feature Extraction and QC Chart Tool Software
The Feature Extraction and QC Chart Tool software is removed by running the Uninstall Agilent Feature Extraction program. Alternatively, you can use the Windows Control Panel to remove the Agilent Feature Extraction software. The uninstaller program removes the Feature Extraction, QC Chart Tool, and MySQL software from your computer.
1 Run the Uninstall Agilent Feature Extraction program in the
The uninstaller wizard starts.
Figure 15 Uninstaller Introduction
2 Click Next.
A warning screen opens.
22 Agilent Feature Extraction Installation Guide
Figure 16 Warning screen
Once you start the software removal process, do not cancel or abort the
uninstaller.
3 Click Next.
A confirmation screen opens.
Figure 17 Confirm and continue screen
4 Click Yes.
CAUTION
Agilent Feature Extraction Installation Guide 23
The software removal begins. When completed, the following message opens.
Figure 18 Uninstall complete
When the software removal is complete, the Uninstall Complete screen notifies you if any errors occurred.
In some cases, the uninstaller cannot remove folders. This occurs when:
You saved FE projects, output files, or images in the installation folder.
You downloaded updated FE protocols from eArray. In this case, the software saves the old protocols in the Old_Protocols folder.
You can remove the folders manually at a later time.
5 Click Done to close the wizard.
24 Agilent Feature Extraction Installation Guide
Getting Help
To get help within Agilent Feature Extraction 12.1
Agilent Feature Extraction 12.1 has several help resources. To open a help guide, from the Agilent Feature Extraction 12.1 menu bar, click the Help. Then select the help you want to display. Help guides are in PDF format, and are opened by default in the Adobe Reader program (if installed).
The following help links are found in the Help menu.
Help command Opens
User Guide Opens the Feature Extraction User Guide, where you can learn about
real time feature extraction, grid templates, protocols, and how to
change image display.
Quick Start Guide Opens the Feature Extraction Quick Start Guide, for an overview of
how Feature Extraction works.
Reference Guide Opens the Feature Extraction Reference Guide, where you learn how
Feature Extraction generates results. It also contains details about
default protocol settings, QC reports, data output, algorithms, and
Command-Line Feature Extraction.
Technical Support Opens the Agilent Contact Us website, where you can find contact
information for assistance with various issues.
Feature Extraction
Training
Opens the Feature Extraction Tutorials website, where you can open
and view tutorials on how to use the Feature Extraction program.
Feature Extraction on the
Web
Opens a menu with the following links:
Array Annotation Opens the list of Agilent catalog gene list web
page, where you can download gene lists for Agilent catalog
microarrays.
Feature Extraction Software Opens the Agilent Feature
Extraction webpage, where you can find related resources and
literature or find other services and products.
Feature Extraction Protocols Opens the Feature Extraction
protocols web page, where you can download protocols for current
and previous versions of Feature Extraction.
Agilent Feature Extraction Installation Guide 25
To contact Agilent Technical Support Technical support is available by phone and/or e- mail message. Various useful information is also available on the Agilent Technical Support website.
Agilent License Opens the Agilent Software License Redemption website, where you
can use your Software Entitlement Certificate to obtain your software
license.
Memory Status Opens the Memory Status display that shows the total and available
memory for your computer.
About Opens the About FE dialog box, where you can find the status of your
Feature Extraction license, computer Host ID, and program version
numbers. (You need the Host ID to redeem your license.)
Help command Opens
In the United States and
Canada)
Telephone: 800-227-9770
E-mail message: informatics_support@agilent.com
Worldwide 1 Go to www.agilent.com/en/contact-us/page.
2 Under Worldwide Sales and Support, click to select a country.
Complete e-mail message and telephone contact information for
your country is displayed.
26 Agilent Feature Extraction Installation Guide
www.agilent
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