Volcano Plot of Microarray data

Select menu: Stats | Microarrays | Display | Volcano Plot

Use this to display volcano plot. For a volcano plot the Y variate is typically a probability (in which case a -log₁₀ transform is used) or less commonly a t-value. The X variate is usually a measure of differential expression such as a log-ratio.

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

You can set additional Options before running.

Available data

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

Y variate

The variate to be plot on the Y axis. This will normally be a probability or a t-value. Double click variates in the in the Available data when this field has focus to enter an item in to this field.

X variate

The variate to be plot on the X axis. This will normally be a log-ratio or other measure of differential expression. Double click variates in the in the Available data when this field has focus to enter an item in to this field.

Shade by

A variate or factor used to colour the points on the graph. This is optional, and if a variate is given, then the following percentiles classes of the variate will be used. The number of groups to shade for a variate is specified in the Options dialog. Double-click a variate or factor in the in the Available data when this field has focus to enter an item in to this field.

Y transformation

Lets you select whether to use a transformation. Select None if you do not want to transform the Y values. Alternatively, select -Log10(Y) to transform the Y values using the -log₁₀ transformation. This transformation is appropriate if the y values are a probabilities. The calculation for this using Genstat’s command language is:

CALC LogY = -LOG10(Y)

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 volcano plot.
Defaults	Reset options to their default settings. Clicking the right mouse on this button produces a shortcut 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.

Example

The following menu uses the file TimeCourse_Estimates.GSH to show the volcano plot of the probabilities of one contrast plotted against the contrast differential expression, shaded by 10 categories, based on the probability of a second contrast. The probabilities are transformed using -log₁₀.

The data is entered into the dialog as follows:

The options are set up:

Giving the resulting graph: