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All core analyses will be conducted with and without imputation for individual variables, including variables that will be imputed at the level measurement, that is, before aggregation to form hospital-level measures.
Missing values were imputed at the level of the scale by means of multiple imputations.
To prevent bias in the survey due to the fact that the missing data was not completely random, missing data was multiply imputed at the National Center for Health Statistics as described in the technical documentation available on the above referenced website.
Missing values were imputed at the protein abundance level using a regularized expectation-maximization algorithm [ 25].
Missing patient reported outcomes will not be imputed at the follow-up time points for the primary analyses.
Second, missings can be imputed at the time the data are phased (Delaneau et al. 2014) or by the use of external reference panels (Howie et al. 2009).
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Given this evidence, we decided to attempt replication of the best-associated markers (whether directly genotyped or imputed) at these 24 loci in an independent Spanish cohort (Phase II).
Values below the detection limit were imputed at half the lower limit of detection for each biomarker.
For individuals with levels below this limit, genistein concentrations were imputed at half the lower limit of detection, that is, 0.05 ng/ml.
34 We applied multivariate imputation based on sex, age, ethnicity, socioeconomic status, health behaviours, body mass index, and biological markers at the preceding phase to impute missing values on health behaviours, body mass index, or biological risk markers at phases 3, 5, and 7. Twentypercentnt of the participants had at least one value imputed at one of the follow-ups.
The genotypes of 2 149 individuals were imputed at over 2 million SNPs using the CEU HapMap samples and the IMPUTE program [40].
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