A summary of the image signal data, detection calls and gene annotations for every gene interrogated on the arrays was generated using the Affymetrix Statistical Algorithm MAS 5.0 (GCOS v1.3) (scaling factor = 1500) and quantile normalization across samples was applied. Log2 transformation and mean-centered standardization was further performed. For genes with multiple probes on the chip, signal intensities were averaged. Each probe ID was converted and collapsed into gene symbols (http://www.genenames.org/). The final 15391 genes that were reliably detected on at least 80% of the arrays with a signal intensity of 64 or greater were used for further analysis.
