geWorkbench

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
  • Affy Excel or txt data file - formats for single Affymetrix experiments (not supported).
  • 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, produced by the program RMAExpress.

• • Genepix files - Produced by a popular analysis program for two color arrays.
• Other
  • FASTA files. DNA or protein sequence files in FASTA format.
  • Pattern files - sequence motifs produced using the Pattern Discovery component of geWorkbench.
  • Genotypic data files - (not supported).

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 Affymetrix 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 already 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.

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.

The result is a new data node containing the merged data. The original data nodes are still present.

Renaming a project or a data node

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 Okay 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 Okay button.

Removing a project or a data node

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

1. Right-click on data nodes 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.

Working with remote data sources

The remote Open File dialog

geWorkbench can retrieve data from certain remote data sources, for example instances of the NCI's caArray database. The Open File dialog allows remote sources to be added to the list of those available either manually or through discovery using grid services. Entries (locations, parameters) for non-grid services can be edited.

As before, right-click on Project which will bring up the Open File dialog. Click the Remote radio button. The Open File dialog window will be expanded to include remote sources.

Four additional buttons appear. They are:

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.

Loading data from a remote instance of caArray

Click on the Go button next to the caArray data source at the bottom of the dialog. All available caArray experiments will be displayed.

Select an experiment that has bioassays. Here we depict the experiment ending in *99049. The number of derived bioassays, 12, is displayed, along with the experiment information. (A new dataset, "Public Rembrandt" has subsequently been added, which would also be good to use for experimenting with caArray data download. It has 53 bioassays available).

To retrieve the bioassays themselves, right click on the experiment and press Get bioassays. This will download the list of available bioassays into geWorkbench.

To actually retrieve bioassay data, select the desired arrays and push the Open button. (Although below we show retrieving multiple array datasets, you might want to first select just one, as each can take several minutes to download).

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

The specification of the remote resource can be edited.

1. Click on the Edit button at the bottom of the Open File dialog.

2. Make the changes that you need.

3. Click on the OK button