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Histograms of Microarray data

Select menu: Stats | Microarrays | Explore | Histograms

Use this 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.

  1. After you have imported your data, from the menu select 
    Stats | Microarrays | Explore | Histograms.
  2. Fill in the fields as required then click Run.

You can set additional Options before running the analysis.

Available data

This lists data structures appropriate for the field which currently has focus. You can double-click a name to enter it in the currently selected field or type the name.

Variates to plot

You can transfer multiple selections from Available data by holding the Ctrl key on your keyboard while selecting items, then click to move them all across in one action. 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:



The factor that identifies the slides. If just a single slide is being displayed you do not need to provide this.

Subset of slides to plot

Lets you 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 must 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 dialog without further changes.
Options Opens a dialog where additional options and settings can be specified for the graphs.
Defaults Reset options to their default settings. Clicking the right mouse on this button produces a shortcut where you can choose to set the options using the currently stored defaults or the Genstat default settings.

Action Icons

Pin Controls whether to keep the dialog open when you click Run. When the pin is up  the dialog will remain open, otherwise when the pin is down  the dialog will close.
Restore Restore names into edit fields and default settings.
Graphics Output Controls how graphs are to be drawn. You can either draw the graph in the Graphics View or save direct to files (JPEG, TIFF, EPS, EMF, GMF, BMP or PNG).
Clear Clear all fields and list boxes.
Help Open the Help topic for this dialog.


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 dialog as follows:

The options are set up:

Giving the resulting graph:


See also

Updated on June 10, 2019

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