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

### Options

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

`COLOURS` = text, scalar or variate |
Colours to use for the plots; default `!t(blue,red)` |

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

`TRANSFORMATION` = string token |
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 text, scalar or variate to define the colours to use for the plots. The default of `!t(blue,red)`

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`

.

### See also

Procedures: `DPROBABILITY`

, `FDRBONFERRONI`

, `FDRMIXTURE`

.

Commands for: Microarray data, Graphics.

### Example

CAPTION 'MAVOLCANO example'; STYLE=meta ENQUIRE CHANNEL=-1; EXIST=check; NAME=\ '%GENDIR%/Data/Microarrays/ApoAIKnockOutEffects.GSH' IF check SPLOAD '%GENDIR%/Data/Microarrays/ApoAIKnockOutEffects.GSH' MAVOLCANO [TRANSFORMATION=log10; NGROUPS=10;\ TITLE='APO Knock-out Mouse Expt KO vs Normal';\ YTITLE='-Log10(Probability)'; XTITLE='Knock-out log-Ratio']\ Y=PrCon[1]; X=Cont[1]; Z=Res_SD ELSE CAPTION 'Microarray example datasets have not been installed.' ENDIF