Spatial Plot of Microarray data

Available Data

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

Variates to plot

A list of the variates to be plotted. Use the arrow

to transfer selected variates in the Available data list to this list. You can use the usual edit functions and keys to add, delete and change names in this list.

Slide Rows

A factor that indexes the rows across the whole slide.

Slide Columns

A factor that indexes the columns across the whole slide.

Slides

The factor that identifies the slides. If just a single slide is being displayed, this does not needed to be provided.

Subset of Slides to Plot

Allows you to specify a subset of the slides from the data set to be plotted. To plot a subset of slides you can specify a list of the levels or labels of the slides factor. For a list of factor levels or labels the numbers or labels should be separated by either spaces or commas. Note that for a list of factor labels where one or more of labels contain a non-alphanumeric character (space, -, + etc...) in the name the label(s) must be specified within single quotes. For example, 'MS 1','MS-2', 'MS+3'.

Action Buttons

Run	Generate the graphs.
Cancel	Close the menu without further changes.
Options	Opens a dialog where additional options and settings can be specified for the graphs.
Defaults	Set 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 plotting of a the log-ratios of a single slide.

The graph titles and colours where set using the Spatial Plot Options dialog.

This is the resulting graph:

High values are shown in red, low values in blue and mid range values in the mix of blue and red are purple. Missing values are displayed in black.