geWorkbench

Outline

In this tutorial, you will learn how to:

• Create a new Project.
• Rename a project and/or project node.
• Remove a project and/or project node.
• Save project files that you have created.

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.

Microrray data and merging

When working with microarray data, all data to be analyzed must be present within one data node in a project. If the data exists as multiple files containing results from single arrays, the data must be merged into a single node before it can be used. geWorkbench can perform this merging step either at the time data is read in, or later in a separate step. Once merged, such a dataset can be saved to disk; it will be saved in the geWorkbench matrix file format.

Supported data formats

• Microarray
  • Affymetrix MAS5/GCOS files - produced by the Affymetrix data analysis programs.
  • Affymetrix File Matrix - a spreadsheet-type multi-experiment format; this is the native file type created by geWorkbench from merged datasets.
  • Tab-delimited text (RMAExpress file) - A simple columnar file format, as produced by the program RMAExpress.
  • Genepix .GPR files - Produced by a popular analysis program for two-color microarrays.
  • Affymetrix CEL files - these files of probe level data can be viewed graphically in geWorkbench but not used directly for analysis.
• Other
  • FASTA files. DNA or amino-acid sequence files in FASTA format.
  • PDB files - protein 3-dimensional structure files can be viewed in the JMol Viewer in geWorkbench.
  • NetBoost Edge List - used by a component still under development.

Tutorial: Working with Projects

Creating a new project

All data must belong to a project. Right-click on the Workspace entry in the Project Folders window at upper left to create a new project.

Renaming a project

1. Right-click on Project folder.

2. Select Rename.

3. In the pop-up screen rename your project.

4. Click on the OK button

Renaming a project data node

1. Right-click on a Project Folder data node.

2. Select Rename.

3. In the pop-up screen rename your data node.

4. Click on the OK button.

Removing a project

1. Right-click on Project folder.

2. Select Remove.

Removing a project data node

1. Right-click on the data node.

2. Select Remove.

Saving a data node to a file

It is here that, among other things, you can create the matrix multi-experiment file format used by geWorkbench from a merged dataset.

1. Right-click on data node that you want to save.

2. Click Save.

A standard file Save screen will come up.

3. Choose a location.

4. Enter a name.

5. Click on the Save button.