Microarray Data Processing: Affymetrix

Raw data

Affymetrix Chips are scanned with the Affymetrix Scanner and images are quantified by the Affymetrix GeneChip Command Console (AGCC) software. Quantified images are stored in the Affymetrix CEL file format.

Background Correction and Probe Set Summarization

B-Fabric applications start from the CEL files and computes expression values using the RMA algorithm (Rafael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. Cope, Bridget Hobbs and Terence P. Speed (2003), Summaries of Affymetrix GeneChip probe level data Nucleic Acids Research 31(4):e15). It either uses the implementation in the Bioconductor package "affy" or the implementation provided by the Affymetrix Power Tools (APT).
The RMA algorithm provides probe-level normalization, background subtraction and probe-set summarization in one step.

Differential Expression

Please see the Two Groups Analysis (Microarray) page.