MA Plots (Loess Normalization)

The MA Plots tab is shown below:

The MA Plots tab contains the following elements:

•

A series of MA plots.

These plots are used to show whether normalization should be carried out prior to data analysis. In the example shown here, a pair of plots is generated for each column; plots on the left and right were generated before and after normalization, respectively. The red spline indicates the mean differences in expression.

A standard assumption in microarray experiments is that few genes should exhibit a change in expression, meaning that most points on the y axis should be close to zero (0) and the spline should be relatively flat. The observed deviation in the splines in the raw data (left plots) was significantly reduced by the normalization performed here.

See MA Plot for more details about these plots.