Microarray Density Plot

Select menu: Stats | Microarrays | Explore | Density Plot

Use this to plot the empirical cumulative probability density function (CDF) or probability density function (PDF) as estimated by a kernel smooth for a variate over a set of slides. The kernel density smoothing is performed using the method outlined by the KERNELDENSITY procedure.

After you have imported your data, from the menu select
Stats | Microarrays | Explore | Density.
Fill in the fields as required then click Run.

You can set additional Options before generating the graph.

Available data

This lists data structures appropriate for the field which currently has focus. You can double-click a name to enter it in the field.

Data variate

The variate containing the data whose CDF or PDF is to be plotted.

Slides

The factor that identifies the slides. If this is left blank a single CDF/PDF plot will be produced for all of the data.

Use log (base 2) transformation

When selected, the Data variate is transformed using log (base 2) before plotting. The calculation for the transformation using Genstat command language is:

CALC LogY = LOG(Y)/LOG(2)

Action buttons

Run	Generate the graphs.
Cancel	Close the dialog without further changes.
Options	Opens a dialog where additional options and settings can be specified for the graphs.
Defaults	Reset options to their default settings. Clicking the right mouse on this button produces a pop-up menu where you can choose to set the options using the currently stored defaults or the Genstat default settings.

Action Icons

	Pin	Controls whether to keep the dialog open when you click Run. When the pin is up the dialog will remain open, otherwise when the pin is down the dialog will close.
	Restore	Restore names into edit fields and default settings.
	Graphics Output	Controls how graphs are to be drawn. You can either draw the graph in the Graphics View or save direct to files (JPEG, TIFF, EPS, EMF, GMF, BMP or PNG).
	Clear	Clear all fields and list boxes.
	Help	Open the Help topic for this dialog.