This menu can be used to plot histograms of microarray data or transformed data using
log base 2 to display densities. 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.
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.
Use Log (base 2) Transformation
The variates to plot are log 2 transformed before plotting. The calculation for the transformation using the GenStat 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
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 where you can choose to set
the menu using the currently stored defaults or the GenStat default settings. |
Example
The following menu shows the histograms of the log 2 transformed foreground means
(in F1Mean) for a subset of 9 slides in the experiment.
The data is entered into the menu as follows:
The options are set up:
Giving the resulting graph:
See Also