Learn to navigate eArray

eArray organizes functions in tabs, pages, and panes. In general, when you click a tab, a specific page appears. Each page contains a group of related settings and commands.

Note:
• As you use eArray, do not click the Back button in your browser, since this can cause eArray to behave unpredictably.

• If you are a guest user, you have access to a subset of the eArray tools — see How do I register to obtain an eArray account

This help topic contains the following sections:

eArray main tabs

Your individual user workspace

Taking action on data items

The Collaboration tab

Collaboration workspaces

eArray main tabs

eArray's functions are organized under three main tabs: Workspace, Collaboration, and Public.

Tab	Description
Workspace	This tab lets you create and manage microarrays and SureSelect Target Enrichment libraries as an individual user. It also gives you access to your personal information, password, and user preferences settings. If you are a workgroup administrator, you access user management functions in the My Functions tab within the Workspace tab.
Collaboration	This tab lets you create and manage content within collaborations. It also gives you access to specific collaboration workspaces, and lets you create, participate in, and manage them.
Public	This tab lets you work with public pages that you have published on eArray. To access public eArray content published by other users, see View published public pages.

main_tabs_(2).gif

Important: Set the Application Type before you begin your work in eArray. Content as well as program functions are partitioned according to the application type to which they apply. See Set application type.

Your individual user workspace

When you click the Workspace tab, your individual user workspace opens, with its own set of tabs (see image above). Initially, the Home tab is selected.

Each tab gives you access to specific eArray functions. The available content and options vary by application type.

Tab	Main functions available
Home	Search – Provides convenient access to many of eArray's search functions without having to navigate to the specific tabs where these functions are otherwise located. Pending Jobs – Lets you monitor the status of jobs that you have submitted to eArray, and to take action on them. This pane pertains only to eArray tasks that are computation- or data-intensive and require time to process.. Click View All to see the complete list, and Refresh to update the list to its most current version. Design Wizards – Provides links to wizards that lead you through a specific microarray creation method. See Use a wizard to create a microarray design/set. Click View All to see the complete list of in-progress wizards, and Refresh to update the list to its most current version. My Designs – Displays the completed microarray designs that you have submitted to Agilent Manufacturing. You can download and request quotes for them, and publish them to the eArray Public page. If you have previously purchased products from Agilent, you can also buy microarrays from the Agilent Online Store through eArray. Click View All to see the complete list, and Refresh to update the list to its most current version.
Microarray	Search – Produces a list of microarray designs or sets that match your search criteria. This list is a gateway to many actions you can take on microarray designs and sets in eArray. Create Microarray – Gives you access to the microarray design wizards for your specific application type. Browse Microarray Designs – Produces a list of microarray designs based on specific folders or categories you select. This list is also a gateway to many actions you can take on microarray designs and sets in eArray. Browse Microarray Sets – Produces a list of microarray sets based on specific folders or categories you select. This list is also a gateway to many actions that you can take on microarray sets in eArray. Express Array – Lets you upload a file of probes and submit it directly to Agilent Manufacturing. This feature is available for the CGH, ChIP, and Expression application types. Notification – Shows a list of microarrays for which you have requested design update notification. You can also cancel or reinstate your subscriptions. Array Calculator – Opens the eArray Array Calculator in a new window. It lets you calculate the number of microarray slides required for a specific design, as well as other relevant array statistics. Request Quote – Lets you submit a quote request for a specific microarray design or set. If you have previously purchased products from Agilent, this link also lets you buy microarrays from the Agilent Online Store through eArray.
Probe Group	Search – Produces a list of probe groups that match your search criteria. This list is a gateway to many actions that you can take on probe groups in eArray. Browse Probe Groups – Produces a list of probe groups based on specific folders or categories that you select. This list is also a gateway to many actions that you can take on probe groups in eArray.
Probe	Search – Gives you access to many different methods for searching eArray's probe databases. Upload – Transfers probes from your computer to eArray. This feature is available for all application types except microRNA. Simple Tiling – Creates Expression type probes that span uploaded target sequences at even intervals. Genomic Tiling – Creates probes for CGH, ChIP, and SureSelect Capture Array applications that span regions of Agilent genomic sequence data at even intervals GE Probe Design – Creates Expression type probes from uploaded target sequence data. GE Probe Check – Analyzes Expression type probes to see if they will work on the Agilent platform, with Agilent protocols. Also analyzes probes to determine potential targets and cross-hybridization problems. Re-annotate – Accepts either probe groups or an uploaded file of probes. Produces a downloadable file that contains the probes, with updated annotation from public databases. This feature is available for the Expression and CGH application types. DNA Analytics Download – Lets you download supplementary files for use in the Agilent DNA Analytics program. This feature is available for the CGH and ChIP application types. GeneSpring Download – Lets you download supplementary files for use in the Agilent GeneSpring program. this feature is available for the Expression application type. Probe Score – Calculates probe performance scores for non-Agilent probes in CGH and ChIP type probe groups. The higher the score, the greater the likelihood that a probe will produce a good log ratio response when it is used in a CGH or ChIP microarray on the Agilent platform.
My Functions	This tab is available to workgroup administrators only. Users – Search users, edit user information, access privileges, and passwords. Create, enable, disable, and delete users. Browse Structure – Set up categories and subcategories for eArray's probe group and microarray design/set browsing functions.
My Account	Personal Info – Change your own contact information or password. Manage Folders – Add, delete, or rename subfolders. User Preferences – Customize default search parameters and the column content of search results pages. You can also create custom probe filters and manage them.
Site Maintenance	This tab is available to workgroup administrators only. Active Sessions – View a list of users in your workgroup who are logged in to eArray.

Note: The features that are available for baits, bait groups, and libraries in the SureSelect Target Enrichment and SureSelect RNA Enrichment application types are described in the help chapter Using eArray to Create SureSelect Enrichment Libraries. The features that are available for libraries and oligo sets in the Mutagenesis application type are described in the help chapter Using eArray to Create Oligo Libraries for QuikChange Mutagenesis.

Taking action on content items

To take action on content items, you first search or browse for the items. You then apply actions to the desired items. Links in the Actions column of search results apply to a specific item in the list. Buttons usually apply to all of the items that you select from the list. You can also restrict search results, and navigate through them page by page. The example below shows the results from a probe group search.

The Collaboration tab

For more information on collaborations, see Collaborate with others in eArray. When you click the Collaboration tab, the collaboration main page opens:

The collaboration main page includes four panes:

Pane	Description
Ongoing Collaborations	List of your current collaborations. You use this pane to take action on a specific collaboration. You can: enter (View) its workspace, invite people to join it, unsubscribe yourself from it, and if you are a lead, dissolve it. You can also create a new collaboration.
Search Collaboration	Find an existing collaboration based on its name, description, keywords, or status. For more information, see Search collaborations.
Invitations to Me	List of collaborations to which you have been invited. You accept or reject these invitations from this pane.
Invitations Sent by Me	List of invitations that you have sent to other people, and their status. If you are a collaboration lead, you can also resend or revoke invitations.

Collaboration workspaces

After you open a specific collaboration workspace from the collaboration main page, a set of collaboration workspace tabs appears. They provide most of the same functionality within the collaboration as you have in your individual user workspace.

The My Account tab within a collaboration is different from the one in your individual user workspace, and offers the following options. Some of the options are only available to collaboration lead(s).

Command	Description
Invite Users	Send e-mail invitations to potential collaborators.
Manage Invitations	(Collaboration lead(s) only) Search for and take action on invitations to the collaboration.
Manage Users	(Collaboration lead(s) only) Assign roles to collaborators or remove a user from the collaboration.
Manage Folders	Add, delete, or rename folders within the collaboration.
Exit Collaboration	Leave the collaboration workspace and return to the collaboration main page.
User Preferences	Sets your user preferences for the collaboration.

Collaboration Leads also have an additional My Functions tab that contains a Browse Structure option. This option allows a lead to set up categories within the collaboration so participants can browse its probe groups and microarray designs/sets.