RMA is a popular model-based approach to normalization and calculating gene expression for Affymetrix microarrays. The approach consists of background correction, quantile normalization and a modeling probe-specific effects across multiple arrays using a median-polish method for fitting the model.
The options for this method include:
Finally, you can select the name of the output file to write
expression results. This file is a tab-delimited output file with
columns labeled with CEL file names (without the .CEL extension) and
rows corresponding to probesets. The default is exprs-rma.txt
in the working directory.