geWorkbench

Introduction

The Preferences item in the menu bar allows a number of features of geWorkbench to be configured.

Text Editor

The user can change the default text editor used to view data files. For example, when you right-click on a data node in the Project Folders component, "View in Editor" is one of the options offered.

Visualization

Heat maps, e.g. in the Color Mosaic component, can be displayed using either a relative or an absolute color scheme.

Note - Changing the relative/absolute preference will not take effect until the next time a data set is loaded.

• Absolute
  • Red represents positive expression values, and green represents negative expression values. Black represents a value of zero. The shade represents the expression magnitude as follows:
  • Formal spec: 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 (default)
  • Relative is similar to the setting for Absolute, but each marker is mean-variance normalized first. A Red-Blue color scheme is used, with red representing the highest values and blue the lowest. White represents the marker average.
  • Note - Relative will give odd-looking results if only a small number of arrays are loaded.

GenePix Value Computation

Four methods for calculating a composite expression measurement for each marker in a GenePix file are offered. They combine the foreground and background and mean or median measurements from each channel in different ways.

1. ( F635 Mean - B635 Mean) / (F532 Mean - B532 Mean).
2. ( F635 Median - B635 Median) / (F532 Median - B532 Median).
3. ( F532 Mean - B532 Mean) / (F635 Mean - B635 Mean).
4. ( F532 Median - B532 Median) / (F635 Median - B635 Median).

See the entry GenePix Format in the GenePix tutorial chapter for further details of processing GenePix data on input.

Remote Components URL

geWorkbench can download certain components from a network repository. This specifies the location of the network component repository.

Marker Load Options

When a microarray dataset is loaded, along with its annotation file, it is possible to re-sort the markers at the global level - the new order will then be seen in all geWorkbench components. There are three options:

• Load markers in the original order
• Load markers ordered by gene name
• Load markers ordered by probeset id

If the Marker Load option is changed, it will take effect the next time a dataset is loaded.

In addition to this global sorting, markers can also be sorted by the same three methods in the Markers component (right-click on the marker list).

Remote Workspaces URL

Development versions of geWorkbench have a feature which allows a workspace to be saved to a remote server for later retrieval or sharing.