MAVOLCANO procedure

Produces volcano plots of microarray data (D.B. Baird).


Options

NGROUPS = scalar
Number of groupings for a Z variate; default 10

COLOURS = scalar or variate
Colours to use for the plots; default !(4,2)

SYMBOL = scalar
Symbol to use for the points; default 1

TRANSFORMATION = string
Whether to transform data to logarithms base 2 (log10, none); default log10

TITLE = text
Title for the graph

YTITLE = text
Title for the y-axis

XTITLE = text
Title for the x-axis

WINDOW = scalar
Window number for the graphs; default 3

KEYWINDOW = scalar
Window number for the graphs; default 0

DEVICE = scalar
Device number on which to plot the graphs

GRAPHICSFILE = text
What graphics filename template to use to save the graphs; default *


Parameters

X = variates
X-coordinates

Y = variates or factors
Y-coordinates

Z = variates or factors
Z-coordinates


Description

MAVOLCANO produces volcano plots of microarray data. The y-coordinates are specified by the Y parameter. Typically these are probabilities, in which case they are usually transformed to -log10(Y). This transformation is thus applied by default, but you can set option TRANSFORMATION=none to suppress it. Less commonly the y-coordinates may be t-values. The x-coordinates are specified by the X parameter. These are usually measures of differential expression such as log-ratios.

   The Z parameter can specify a variate or factor to use to colour the points on the graph. If this is a variate, the values are grouped into the number of percentiles specified by the NGROUPS option. The COLOURS option supplies a scalar or variate to define the colours to use for the plots. The default of !(4,2) uses colours ranging from blue to red. The SYMBOL option defines the symbol to use for the points (default 1).

   The TITLE, YTITLE and XTITLE options can supply titles for the graph, the y-axis and the x-axis, respectively. The WINDOW option specifies the window to use (by default 3), and the KEYWINDOW option can specify a window for a key (by default there is none). You can use the DEVICE option to plot to a device other than the screen. The GRAPHICSFILE option specifies then supplies a template for the file names.

 

Options: NGROUPS, COLOURS, SYMBOL, TRANSFORMATION, TITLE, YTITLE, XTITLE, WINDOW, KEYWINDOW, DEVICE, GRAPHICSFILE.

Parameters: X, Y, Z.


Action with RESTRICT

MAVOLCANO takes account of any restrictions on X, Y or Z.