geWorkbench

Getting Started

These tutorials assume that you have successfully completed the installation instructions. If you haven't installed the entire program, please go Download and follow the installation instructions.

In this tutorial you will learn how to:

• Start the application
• The GUI Elements of the System

Loading Data

In this tutorial, you will learn how to:

• Create a New Project.
• Merge Data from several Loaded Microarray Experiments.
• Rename a Project and/or Project Node.
• Remove a Project and/or Project Node.
• Load, Add, and/or Modify Remote Data.

Before you can continue, geworkbench should be running. For help with this, please refer to the Getting Started (insertlink) section. The file cardiomyopathy.exp should be used in this tutorial.

There are different types of Array files that you can use when loading data

• Affy Excel or txt data file. brief explanation of file type needed
• Affymetrix MAS5/GCOS Files.This one will be used for the tutorial. brief explanation of file type needed
• Affymetrix File Matrix. brief explanation of file type needed
• RMA Express Processed File. brief explanation of file type needed
• Genepix Files. brief explanation of file type needed
• Genotypic data Files. brief explanation of file type needed
• Fasta Files. brief explanation of file type needed
• Pattern Files. brief explanation of file type needed
• Normalized no-confidence expression matrix. brief explanation of file type needed

1. To create a New Project right mouse click on workspace.

2. Left mouse click on Project.

3. Project folder will open, right mouse click on Project folder, left mouse click on open files.

4. Find the type of file that you want to work with. In this case it will be Affymetrix MAS5/GCOS Files.

5. Find the file that you want to work with and select.

6. Make sure Local radial button is selected.

7. Click on the Open button.

Your File is now loaded:

You Can Merge Data From Several Loaded Microarray Experiments Into One Project Folder

As long as files are of the same type you can merge them into a project folder. You can do this during the original loading process, or after you have already loaded a file.

To Merge Data From The Original Loading Process

1. Right mouse click on the Project folder.

2. Select the files that you want to Merge.

3. Select the Merge Files box.

4. Left mouse click on the Open button.

Your File Nodes will now be Merged into one Project folder.

To Merge Data From Experiments Already Loaded

1. Select the Project Nodes that you want to Merge.

2. Left click on file, choose Merge Datasets.

You Can Rename a Project and/or a Project Node

Renaming A Project

1. Right mouse click on Project folder.

2. Select Rename.

3. In Pop-up Screen Rename your Project.

4. Click on the Okay button

Renaming a Project Node

1. Right mouse click on Project Node.

2. Select Rename.

3. In Pop-up Screen Rename your Project Node.

4. Click on the Okay button.

You Can Remove a Project and/or a Project Node

Removing A Project

1. Right mouse click on Project folder.

2. Select Remove.

3. You will no longer see the Project folder.

Removing a Project Node

1. Right mouse click on Project Node.

2. Select Remove Project.

3. You will no longer see the Project Node.

Load, Add, and/or Modify Remote Data