Revision as of 19:27, 11 March 2011 (view source) Smith (talk | contribs) (→‎Save) ← Older edit		Revision as of 19:31, 11 March 2011 (view source) Smith (talk | contribs) (→‎Save) Newer edit →
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	===Save===		===Save===
−	It is here that, among other things, you can create the matrix multi-experiment file format used by geWorkbench from a merged dataset	+	A data set can be saved back to a file on disk.
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		+	If the selected data set is a microarray gene expression data set, it will be saved in the geWorkbench ".exp" format, which preserves any array sets that may have been defined.  Merged data sets can be saved together in this way.

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Revision as of 19:31, 11 March 2011

Home | Quick Start | Basics | Menu Bar | Preferences | Component Configuration Manager | Workspace | Information Panel | Local Data Files | File Formats | caArray | Array Sets | Marker Sets | Microarray Dataset Viewers | Filtering | Normalization | Tutorial Data | geWorkbench-web Tutorials

Analysis Framework | ANOVA | ARACNe | BLAST | Cellular Networks KnowledgeBase | CeRNA/Hermes Query | Classification (KNN, WV) | Color Mosaic | Consensus Clustering | Cytoscape | Cupid | DeMAND | Expression Value Distribution | Fold-Change | Gene Ontology Term Analysis | Gene Ontology Viewer | GenomeSpace | genSpace | Grid Services | GSEA | Hierarchical Clustering | IDEA | Jmol | K-Means Clustering | LINCS Query | Marker Annotations | MarkUs | Master Regulator Analysis | (MRA-FET Method) | (MRA-MARINa Method) | MatrixREDUCE | MINDy | Pattern Discovery | PCA | Promoter Analysis | Pudge | SAM | Sequence Retriever | SkyBase | SkyLine | SOM | SVM | T-Test | Viper Analysis | Volcano Plot

Workspaces and Projects

In the Project Folders component there is a top-level object called a workspace.

The workspace can contain one or more separate projects, and each project can contain opened data files and analysis results. An analogy might be that a workspace is like a drawer in a filing cabinet, and projects are individual folders in that drawer. Projects allow data to be grouped, for example by experiment. A project can contain many different types of data, for example microarray data, FASTA sequence files and graphical images. The workspace as a whole, with all its projects and data nodes, can be saved and restored. However, only one workspace can be open at one time.

All data must belong to a project.

Creating a new project

There are two ways to create a new project. First, select the Workspace node in the Project Folders component. Then, either

(1) In the top-level Menu, select File->New->Project.

or,

(2) In the Project Folders component, right-click on the Workspace and select "New Project".

Either way, the new Project is placed into the workspace:

Project Menu Options

Right-clicking on a Project node gives a menu with the following options

Open Files

• Loading data from local files is covered in the chapter Local Data Files
• Retrieving data from remote sources (caArray) is covered in Remote Data Sources

Open PDB File from RCSB Protein Data Bank

If Open PDB File from RCSB Protein Data Bank is chosen, a dialog box appears.

Type in the name of a PDB structure entry and it will be retrieved from the RCSB Protein Data Bank and loaded into geWorkbench.

Rename

A dialog box will appear in which to enter a new name for the project.

Remove

Selecting Remove will remove the project and all of its data nodes.

Project Data Node Menu Options

Right-clicking on a project data node will produce a popup menu with the following options:

Save

A data set can be saved back to a file on disk.

If the selected data set is a microarray gene expression data set, it will be saved in the geWorkbench ".exp" format, which preserves any array sets that may have been defined. Merged data sets can be saved together in this way.

A standard file Save screen will come up.

1. Choose a location.

2. Enter a name.

3. Click on the Save button.

Rename

A dialog box will appear in which a new name can be entered.

Remove

The selected data node and any child data nodes it may have will be removed.