View source for Normalize Affymetrix experiment and control (analysis)

==== Description ====
This procedure takes Affymetrix CEL files as input and returns normalized data. Normalization is carried out using methods in the Bioconductor AFFY package. Individual CEL files are assigned to either test condition (experiment, study, treatment) or control condition.

The first step normalizes test and control measurements altogether and calculates normalized signal values. The default normalization method is MAS5. Several other methods are available for selection.

Next, the table comprising both test and control values is split yielding two tables for each experiment group. The resulting tables, "Experiment normalized" and "Control normalized", can be applied in subsequent next workflows, such as Compute differentially expressed genes and Gene set enrichment analysis.