In approach 2, bootstrap samples over the imputed data could differ by the imputed values as well as the selected subjects.
After SNP imputation, we included the imputed SNPs for the association study.
Similar results were obtained using the imputed or original databases, so only the imputed database was used for its larger effective sample size.
Passive imputation and PMM ensure that the imputed values conform to the known functional relation between the covariates, e.g. that the imputed value of X2 is equal to the square of the imputed value of X.
The imputations from the last iteration form the imputed dataset.
We chose not to report the imputed dataset here because the findings of the imputed data set concurred with the complete case analysis.
These statistics provide a very complete validation set of the imputed data, which assures the coherence of the imputed values regarding the collected data from donors.
For the mixed density datasets, only the observed genotypes and the imputed haplotype index numbers were stored, rather than the imputed genotypes, which greatly decreased storage requirements.
For the imputed data, see Table 2.
Logistic regression results from the imputed data were reasonable.
No significant difference was found between the imputed models and the model shown.
