This menu can be used to produce 2D plots of microarray data or transformed data using log base 2.
You can display separate plots for all slides or use a subset of these. Alternatively,
you can display all the plots within a single graph using a trellis plot.
For each of the plots you can add a reference and mean curve.
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.
Y Variate
The variate(s) to be plotted on the Y axis of the plot.
X Variate
The variate(s) to be plotted on the X axis of the plot.
Use Log (base 2) Transformation
The Y and X variates are log 2 transformed before plotting.
The calculation for this using GenStat's command language is:
CALC LogY = LOG(Y)/LOG(2)
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
If you only want plots of some of the slides in the data set, you can
provide a list of the levels or labels of the slides you want. The
labels should be separated by commas. If the labels have spaces in
them, quote them with single quotes, e.g. 'MS 1','MS 2', 'MS 3'.
Groups within Plots
A factor that indicates groups within each graph which are to be plotted
in different colours.
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 example shows how to plot the foreground means of the red and
green dyes against each other (i.e. F1Mean vs F2Mean), with different print tips
(in factor Slide_block) for a subset of 9 slides in the experiment.
The options have the titles provided, and specify a 1-1 reference line
within a trellis plot.
This produces in the following graph:
See Also