MAQC samples were processed following Affymetrix one-cycle sample preparation protocol with 5 ug of total RNA (Please refer to GeneChip Expression Analysis Technical Manual for details) and hybridized to Human Genome U133 Plus 2.0 array (catalog #900470, #900466 or #900467).
Hybridization protocol
Affymetrix GeneChip Operating Software (GCOS) is used to automate the control of GeneChip Fluidics Stations and Scanners.
Scan protocol
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Description
NA
Data processing
The CEL file data were analyzed with BioConductor to generate probeset level data using the justPlier() function. Probe-level data were quantile normalized before PLIER summarization per test site (20 arrays). An offset value of 16 was then added to each probeset-level data point.