Normalization and Analysis
We used GenePix software (Axon) to obtain backgroundsubtracted intensity values for
each fluorophore for every feature on the array. We normalized the intensities in the IPenriched channel to intensities
in the genomic DNA channel using the median values of the dataset. We then used a single chip error model (Hughes et
al., 2000) to calculate confidence values for each spot on each array (single probe pvalue).
This error model functions by converting the intensity information in both channels to an
X score which is dependent on both the absolute value of intensities and background noise
in each channel.
Replicate data were combined, using the X scores and
ratios of individual replicates to weight each replicate's contribution to a combined X score
and ratio. The X scores for the combined replicate are assumed to be normally distributed
which allows for calculation of a pvalue for the enrichment ratio seen at each feature.
