Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios

Table 2 Comparison of effects on allelic intensity ratios between Illumina BeadStudio and quantile normalized HapMap data.

Platform	HapMap samples	Mean Theta_AB ± mean SD BeadStudio*	Mean Theta_AB ± mean SD QN*	Paired p-value theta SD_QN < SD_BeadStduio **
300 k v1	111	0.581 ± 0.095	0.454 ± 0.087	2.2*10^-16
300 k v2	120	0.595 ± 0.097	0.457 ± 0.086	2.2*10^-16
370 k	123	0.594 ± 0.097	0.460 ± 0.082	2.2*10^-16
550 k	120	0.608 ± 0.099	0.451 ± 0.084	2.2*10^-16

*: The mean and SD of theta was calculated for each sample. The mean of these values for all samples are shown.
**: Paired two-sided t-test. H0: Δ = SD_QN - SD_BeadStudio =0

ISSN: 1471-2105