Volcano Plot of Microarray data
See Also  Example
This menu can be used 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.

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.

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

Allows you to 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

RunGenerate the graphs.
CancelClose the menu without further changes.
OptionsOpens a dialog where additional options and settings can be specified for the volcano plot.
DefaultsSet the menu settings back to the default settings. Clicking the right mouse on this button produces a shortcut menu where you can choose to set the menu using the currently stored defaults or the GenStat default settings.

Example

The following menu shows 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 menu as follows:

The options are set up:

Giving the resulting graph:

See Also