High Pure formalin-fixed, paraffin-embedded tissue (FFPET) RNA Isolation Kit (Roche Molecular Systems, Pleasanton, California)
Label
biotin
Label protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol
Following fragmentation, 5 ug of cRNA were hybridized for 16-18 hr at 47C on GeneChip HG-U133_Plus_2 Genome Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol
GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.
Data processing
Raw microarray data was pre-processed by an internal software tool developed at Roche Molecular Systems Inc., Pleasanton, CA, USA. Specifically, a special DQN signal used the quantities of beta distribution with p = 1.2 and q = 3 for normalization
