Scatter plot

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 | Microarray and Small RNA Analysis (Image expressionfolder)| General Plots | Create Scatter Plot (Image scatterplot)

In the first two dialogs, select two samples ( (Image array), (Image rnaseq) or (Image rnaseqtrack_16_h_p)): the first is the sample that will be plotted on the X axis of the plot, the second the one that will define the Y axis. Clicking Next will display a dialog as shown in figure 29.81.

Image scatter_step2
Figure 29.81: Selecting 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 Finish to start the tool.

For more information about the scatter plot view and how to interpret it, please see Scatter plot view of an experiment.