Settings

The Settings are accessible from the Options menu, and contain Display settings External applications settings.

The Display dialog box contains the following tabs:

Clustering Results View – Contains check boxes that configure the following parameters:

• A common Y-axis scale for all cluster patterns (vs. cluster specific)
• Visible x axis
• Connect all points in a pattern
• Display similarity matrix for probes (using Pearson correlation)
• Display similarity matrix for conditions (using Pearson correlation)

Group Analysis Results View – Contains a check box that configures whether the Y-axis scale of all histograms is common OR cluster specific.

Data Matrix View – Allows selection between:

• Range control and extreme values control when rendering expression matrix values.
• The red/green coloring scheme can be changed to blue/yellow.

The External applications dialog box allows specification of the location of the R executable (required for CEL files loading). In Windows, R.exe file is likely to be located in the 'bin' folder of R software. In Linux, you may type 'which R' in the command line to find R path.