...

The RMA background transform check box applies robust multi-array average (RMA) normalization to your microarray samples [2]. This is a well-accepted method of background correction for microarray intensities.

The Quantile normalization check box performs quantile normalization on all microarray intensities. This is important in making sure that signals from any two arrays are comparable.

Any combination of these advanced options can be saved as its own option set. Once the option set has been created, it will be available in the Option set drop-down menu for use in future projects.

After you have finished configuring all microarray conversion options. Click the Next button to configure the parameters for the aligner you have chosen to use. Please refer to the documentation on Alignment for more information about configuring aligners.

...