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It is known that the sequence profiles are sensitive to factors such as the optical background correction and saturation [18], [28] (see also below).
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All arrays were background corrected using local background correction and normalized using Lowess normalization [ 87].
We used RMA and Bioconductor in R [70] for background correction and normalization [71], [72].
SNP 6.0 CEL files were imported into Partek using default settings for background correction and summarisation.
Generally, background correction and normalization are used to reduce the impact of variations in experimental conditions.
VSN is a protocol that combines the background correction and across array normalization [40].
Background correction and normalization was performed using the robust multi-array average (RMA) algorithm.
The effects of the first three factors were removed through background correction and across array normalization.
RMA background correction and quantile normalization was applied.
Normalization step included Norm-exp background correction and quantile normalization.
These values underwent colour-adjustment, background correction and ssn normalization.
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