Viewing MA plots

The resulting plot is shown in a figure 31.61.

Image ma_before_transform_web
Figure 31.61: MA plot based on original expression values.

The X axis shows the mean expression level of a feature on the two samples and the Y axis shows the difference in expression levels for a feature on the two samples. From the plot shown in figure 31.61 it is clear that the variance increases with the mean. With an MA plot like this, you will often choose to Transform the expression values.

Figure 31.62 shows the same two samples where the MA plot has been created using log2 transformed values.

Image ma_after_transform_web
Figure 31.62: MA plot based on transformed expression values.

The much more symmetric and even spread indicates that the dependance of the variance on the mean is not as strong as it was before transformation.

In the Side Panel to the left, there is a number of options to adjust the view. Under Graph preferences, you can adjust the general properties of the plot.

Below the general preferences, you find the Dot properties preferences, where you can adjust coloring and appearance of the dots:

Note that if you wish to use the same settings next time you open a scatter plot, you need to save the settings of the Side Panel.