Microarray Cluster Probes/Genes Options

Use this to specify options for the Cluster Probes/Genes menu.

Dendrogram

When selected, produces a plot of the dendrogram. Use the Title field to specify a title for the plot. This option is only available when the Clustering method is set to Hierarchical.

Groups response plot

When selected, produces a plot of the profile of each group plotted against slide or target level. The y-axis will be the probe effect, and the x-axis will be the slide or target levels. If the Display mean response per group option is selected, then only the mean of the probes for each group for each slide/target will be plotted, otherwise each probe/gene will be plotted in a range of colours. Use the Title field to specify a title for the groups plot. By default each group is displayed within a separate plot, however, you can display the groups in different panels on a single graph by selecting the Use trellis plot for groups plot option. For a large number of probes, we recommend that the groups mean only be plotted when using the trellis plot option as this can be very memory intensive.

Display

This specifies which items of output are to be produced by the analysis.

Summary	A summary of the data used to generate the similarity matrix
Clustering output	Displays output from the hierarchical or non-hierarchical clustering
Group membership	List of probes and targets that belong to each group generated by the respective cluster analyses

Display cluster groups in a spreadsheet

Create a new spreadsheet containing the probe/gene names, group membership, and effects in columns, sorted by group. The effects columns will be labelled S[1],S[2], … where the first column corresponds to the effects for the first slide or target (as specified by the ordering of the targets/slides factor).

Action buttons

OK	Save the options settings and close the dialog.
Cancel	Close the dialog without making any changes.
Defaults	Reset options to their default settings.

Action Icons

	Clear	Clear all fields and list boxes.
	Help	Open the Help topic for this dialog.