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

Staaf et al. BMC Bioinformatics 2008 9:409   doi:10.1186/1471-2105-9-409