As described in Scatter plot view of an experiment, an experiment can be viewed as a scatter plot. However, you can also create a "stand-alone" scatter plot of two samples:
Toolbox | Transcriptomics Analysis ()| General Plots | Create Scatter Plot ()
Select two samples ( () or ()). Clicking Next will display a dialog as shown in figure 27.106.
Figure 27.106: Selcting which values the scatter plot should be based on.
In this dialog, you select the values to be used for creating the scatter plot (see Selecting transformed and normalized values for analysis).
Click Next if you wish to adjust how to handle the results. If not, click Finish.
For more information about the scatter plot view and how to interpret it, please see Scatter plot view of an experiment.