Exact(2)
Rs12566340 was genotyped in the NZ RA sample set and imputed in the WTCCC RA sample set.
The SNP was genotyped in TwinsUK and imputed in the other samples but was not available in the sample from Talana, so meta-analysis was performed on seven of the eight groups (n = 4322).
Similar(58)
SNP rs360719 was not genotyped by Illumina (as described in the Materials and Methods) because this SNP was <100 bp away from other genotyped SNPs and therefore was genotyped in the UK SLE trios using a Taqman assay and then imputed in the UK|CC cohort.
GCS had 977 missing values; these were considered to be normal (value = 15) and were therefore imputed in the training and the validation sets.
Finally, the 19 SNPs that were genotyped in GEM and the NTR replication sample and measured or imputed in the ATM GWA replication sample were meta-analysed together with the discovery data sets.
Whereas the variability of the reliability coefficients between different samples within single studies (level 2) and the variability between studies (level 3) are estimated by multilevel models, the within-variability (standard error, level 1) must be calculated for each study using the standard error of the reliability coefficient and will be imputed in the multilevel analysis.
All questionnaire data collected through paper forms, are imputed in the database and quality and completeness control are performed weekly.
SNP rs10835638 was well imputed in the data (imputation quality 0.995; HWE P = 0.16; missing rate = 0.3%).
Imputation was carried out on predictor variables only, cases with missing dependant variables were dropped, not imputed, in the MARS and Random Forest analyses.
The ten SNPs were either genotyped by Sequenom MassArray or by Affymetrix SNP array or imputed in the ARIC and FHS datasets.
For D250, there was no significant difference in accuracy of genomic evaluation between the reference scenario (r GEBV, EBV = 0.66) and the scenario where genotypes were imputed in the validation animals (Table 2).
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