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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