geWorkbench

In the this tutorial, you will:

• Get acquainted with the various geWorkbench visualization tools
• View a dataset in geWorkbench
• Modify the visualization preference settings

Visualization Tools

Visualization tools provide a view of the chip(s) under investigation and can be used for ascertaining the quality of the data. Activating gene and phenotype sets (Tutorial - Data Subsets) can be used to restrict the number of markers/arrays displayed. The images created can be saved and exported. A detailed description on how to manipulate visualization components is described in the online help.

Microarray View: Used to inspect each separate microarray using the Array scroll bar. Note that the markers are displayed in the order they appear in the dataset, and the image is not a physical representation of the microarray layout. The image can be saved into the Project Folders component under its parent dataset by right-clicking and selecting Save Image.
Tabular Microarray Viewer: Presents the numerical values of the expression measurements in a table format. One row is created per individual marker/probe and one column per microarray.
Color Mosaic: Heat maps for microarray expression data, organized by phenotypic or gene groupings. The Display button causes the image to be displayed. The Label and Accession buttons display the marker name and accession number to the right of each row. The buttons Pat, Abs and Ratio are not currently used.
Expression Profiles: For each active marker (default is all), a line showing the expression value vs array is graphed. Each marker is displayed with a separate color line. The Plot button must be pushed to draw the display. If a subset of markers has been activated, the number active is shown adjacent to the Markers label. Right-click options are shown.
Scatter Plot: A pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values. The first marker selected serves as the x-axis reference, shown with a dark background; this can also be set by right-clicking and selecting the x-axis marker as shown). Subsequent arrays selected are plotted against this reference in different sub-images. Up to six sub-images can be created. Right-click options are shown in the second picture.

Preparation

Load a microarray dataset. This could be the dataset created in Tutorial - Projects and Data Files, or the file webmatrix.exp that is included with the geWorkbench download.

View a dataset

1. Select the Microarray Viewer visualization component in the View Area at the top-right section of the interface.
2. The All Markers and All Arrays checkboxes can be used to override the effects of activated sets, should they be in use. When no sets are activated, all markers or arrays will be used.

Preferences

The Preferences selection in the Tools menu allows users to specify how certain aspects of the system will behave. Once your preferences are set, these preferences are persistent between application sessions.

Modifying Settings

1. From the main menu, click on Tools>Preferences.

2. In the Preferences pop-up window, you can define settings for:

• Text Editor: The editor selected will be used to open and inspect data sets loaded in a project. Notepad is the default setting.
• Visualization: The color scheme to be applied to color mosaic images.
  • Absolute: (default) Let M = max{|min|, |max|} over all expression measurements, across all arrays. If expression value x > 0, assign it the red spectrum x / M * 256. If expression value x is negative, assign it to the green spectrum -x / M * 256.
  • Relative: This is similar to the setting for Absolute, but each marker is mean-variance normalized first.
• Genepix Value Computation: You can specify how compute the value displayed for Genepix array. The default setting is Option (Mean F635 - Mean B635) / (Mean F532 - Mean B532).

Select Relative for the visualization preference. Note that this choice will not take effect until the next time you load a data set.

3. Click on OK.