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Table 1 Comparison of Log R ratio standard deviations between 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 Log R ratio SD* BeadStudio Mean Log R ratio SD* QN p-value SDQN < SDBeadStudio ** Mean decrease in SD (%) ***
300 k v1 111 0.134 0.136 0.99 0
300 k v2 120 0.197 0.168 2.2*10-16 15
370 k 123 0.262 0.193 2.2*10-16 26
550 k 120 0.209 0.160 2.2*10-16 23
  1. *: The SD of Log R ratio was calculated for each sample. The mean SD for all samples is shown.
  2. **: Paired two-sided t-test. H0: Δ = mean Log R ratio SDQN – mean Log R ratio SDBeadStudio =0
  3. ***: (1- (mean Log R ratio SDQN)/(mean Log R ratio SDBeadStudio))*100