Normalization and Analysis
We used GenePix software (Axon) to obtain background-subtracted intensity values for
each fluorophore for every feature on the array. We normalized the intensities in the IP-enriched 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 p-value).
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 p-value for the enrichment ratio seen at each feature.