Revision as of 21:02, 27 February 2006

Outline

In this tutorial, you will learn how to:

• Create a new Project.
• Load microarray data.
• Merge data from several loaded microarray experiments.
• Rename a project and/or project node.
• Remove a project and/or project node.
• Save project files that you have created.
• Load, add, and/or modify remote data.

Supported data formats

• Microarray
  • Affymetrix MAS5/GCOS Files.This one will be used for the tutorial. brief explanation of file type needed
  • Affymetrix File Matrix - this is the native file type created by geWorkbench.
  • RMA Express File - RMA Express is a sophisticated tool for combining data from multiple Affymetrix chips.
  • Affy Excel or txt data file.
  • Normalized no-confidence expression matrix. A variant of the geWorkbench file matrix format that omits the confidence value columns (P-value or Present/Absent calls).
  • Genepix Files - An analysis program for two color arrays.
• Other
  • FASTA Files. DNA or protein sequence files in FASTA format.
  • Pattern Files.
  • Genotypic data Files.

Loading data files into a project

In this example, we will load 10 individual Affymetrix MAS5 format files, and merge them into a single dataset.

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.

Next, right-click on the new project entry and select Open Files.

Here, we will select file type Affy GCOS/MAS5 as shown.

Make sure to check the Merge files checkbox.

We select 10 MAS5 format text files from the directory geworkbench\data\training\cardiogenomics.med.harvard.edu, which is included in the geWorkbench download.

Click Open.

The chip type HG_U95Av2 is recognized...

The merged dataset is listed in the Project folder. The data is displayed, in single array format, in the Microarray Viewer. Note we have increased the intensity slider to maximum here.

===Merging microarray datafiles after they have been loaded.

If Affymetrix data files are not merged at the time they are read in, they can also be merged later, as long as they are from the same chip type.

To merge data from individual experiments already loaded

1. Select the read-in data files that you want to merge.

2. Click on File in the menu bar, and choose Merge Datasets.

The picture shows the resulting merged dataset created from several individual data files.

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.

Saving a File 'Node'

1. Right mouse click on File(s) 'Node(s)' that you want to save.

2. Click on the Save.

The Save Screen will come up.

3. Choose a location.

4. Name your File(s) 'Node(s)'

5. Click on the Save button

Load, Add, and/or Modify Remote Data

geWorkbench can retrieve data from certain remote datasources, for example instances of the NCI's caArray database.

When the File Screen comes up click on the Remote Radio button and you will see this screen. The Open File Dialog Window is updated so that you can work with your Remote Sources.

The four buttons on the bottom of this screen are what you will be working with

Basic Usage

caArray button - Gives you a listing of your Remote Resources.

Go button - Accesses the Remote Source that you selected.

Add A New Resource button - Opens the Data Source Definition Page used to add Remote Data.

Edit button - Edits Remote Source Parameters.

To Add A Remote Source

1. Click on the Add A New Resource button.

This is the Data Source Definition Page

2. Fill in the Data Source definition page. URL and Short Name are required fields.

3. Click on the OK button.

The configuration is set up to automatically reflect your additional Data Source.

To Modify A Remote Source

1. Select the File that you want to modify.

2. Click on the Edit button.

3. Make the changes that you need.

4. Click on the OK button