Background adjustment, normalization and summarization of probes to the transcript level were performed using the Robust Multichip Average (RMA) method (Irizarry et al., 2003).
Calculations for expression levels were performed using BioD1 software (Vilber Lourmat) without background subtractions.
Calculations for exposure levels were performed using BioD1 software (Vilber Lourmat) without background subtractions.
No background correction was performed, as overall background levels were very low.
The background level was defined as the level at which low level transcription becomes indistinguishable from other background signals.
Therefore spots near the background level have a higher QM if the background level is higher.
Decay and background corrections were performed.
Background corrections were performed by subtracting the background signals from blank samples.
Bias correction and background correction were performed through ProteinPilot.
Background spectra were performed at air or pure KBr pellet.
Preprocessing steps such as background subtraction, probe cell normalization and expression level calculations, were performed using quantile normalization and Robust Microarray Analysis (RMA) software [12].
