geWorkbench

Menu Bar

Introduction

The Menu Bar is located at the top of the geWorkbench graphical interface, and provides access to important actions, settings and information.

This section will briefly cover the individual menu items. Some items have their own more extensive documentation, and links to this will be provided.

The first two items in the menu, "File" and "Edit", apply to the Project Folders component, described in the next section.

Background on the Project Folders component

In brief, the Project Folders component is used for data organization and management. It contains four types of "nodes", arranged in a hierarchical fashion.

• Workspace - A workspace contains all the data for a geWorkbench session. Only one workspace can be present at a time. A workspace can be saved and reloaded. Workspaces are used to hold one or more projects.
• Project - A project is used to hold the data and the analysis results for a particular experiment. A workspace can contain more than one project, and one can easily switch between projects.
• Data nodes - These contain data either loaded from files on disk or retrieved from the network.
• Result nodes - After an analysis is done in geWorkbench, a result node is created as a child of the data node from which it was created.

The following diagram shows the Project Folders component with a single data node and its child t-test analysis result node.

Further details about the Project Folders component can be found in the Projects section.

File

The following choices are available under the File menu.

Open

• File - Open a specific data file from disk. A Project node must be selected in the Project Folders component. A standard file browser will appear, and the user can select from any of the file types that geWorkbench can directly load. If no project node yet exists, one must be created before a data file can be loaded.
• Workspace - Open a previously saved geWorkbench workspace. A standard file browser will appear with which the desired workspace file can be located.

It does not matter what is currently selected in the Project Folders component, as everything will be overwritten by the contents of the newly loaded workspace. As shown in the below figure, a dialog will appear warning the user that the current workspace will be overwritten. The user is offered the option to save the current workspace before proceeding.

Save

• Workspace - Save the current geWorkbench workspace to a file on disk.

New

• Workspace - Create a new workspace in the Project Folders component. Doing so will destroy the existing workspace, so the user will be prompted as to whether to save the current workspace. This is shown in the following diagram.

• Project - Within a workspace, create a new project. Any number of projects can be created in a workspace.

Export

• Export the microarray dataset currently selected in the Project Folders component in the "Affymetrix Matrix File Format" (.exp). This format preserves array sets that may have been defined.

Merge Datasets

If more than one data file originating from the same platform has been loaded into a project, the datasets can be merged into one for analysis. See Local_Data_Files#Microrray_data_and_merging_datasets for further information.

Remove

This option will remove a project or a data node under the project from the Project Folders component. It will not remove a top-level workspace.

Exit

Close geWorkbench. The user will be prompted as to whether to save the workspace before closing.

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