We excluded all metabolites that had imputed value > 20% in the groups we analyzed for the pairwise comparisons.
Excluding families that had imputed data on one or more family members (161 families) also made virtually no difference to the results (data not shown).
Sensitivity analyses evaluated the change in overall study results by removing 1) the RCT by Kanders et al (32) that had imputed SDs for change in the outcome measurements and, in a separate analysis, 2) the RCT by Knopp et al (33) that had an inherently different intervention design (aspartame capsules were provided rather than LCSs in foods or beverages or as tabletop sweeteners).
Second, only SNPs were included that we had imputed data for (mostly in addition to the fingerprint data; rs265981, rs6275, rs1800497, rs6280, rs2519152, and rs4680), resulting in 7,734 individuals with full genotypic and phenotypic data.
Version 1.0 of the eMERGE imputed data set includes more than 13 million single-nucleotide polymorphisms in more than 42,000 samples that have been imputed using the BEAGLE reference panel and the 1000 Genomes cosmopolitan reference panel, October 2011 release.
Keep in mind that in the analysis where single imputation has been applied, some of the observed score values, with respect to monotone missingness, are actually missing values that have been imputed.
The strains we examined from the Saccharomyces Genome Resequencing Project include nucleotides that have been imputed by taking into account phylogenetic relationships between strains to correct likely sequencing errors and fill in missing data (Liti et al. 2008).
This step is similar to Major sub-step 3, with the exception that haplotype libraries are internally built using the information that has been previously imputed.
Figure 4 plots ROC curves (see Methods) for each of the four methods, with single locus regression applied to complete genotype data and resample-based methods applied to genotype data with ∼10% missingness that has been multiply imputed (see Methods and below).
The specific length of a beard, the way it is trimmed, whether or not it is dyed: these distinctions make a deliberate statement about the wearer's religious affiliations and the degree of his piety — or the degree of piety that he wishes to have imputed to him.
