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

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

Platform HapMap samples Mean ThetaAB ± mean SD BeadStudio* Mean ThetaAB ± mean SD QN* Paired p-value theta SDQN < SDBeadStduio **
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
  1. *: The mean and SD of theta was calculated for each sample. The mean of these values for all samples are shown.
  2. **: Paired two-sided t-test. H0: Δ = SDQN - SDBeadStudio =0