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)
Enrichment 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.