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Results from multiply imputed data sets were combined using standard multiple imputation rules (White et al. 2011).
AlphaImpute combines simple phasing and imputation rules, long-range phasing, haplotype libraries, and segregation analysis to impute genotypes of all animals in a pedigree for all genotyped SNP.
The standard combining rules for multiple imputation (the repeated imputation rules) have to be modified because the imputations within a nest are correlated, since they share a common set of imputed values for the first set of missing values.
Refer to Dite et al (2003), 2010 for more detailed descriptions of the imputation rules.
However, a limitation of the RAPID-PsA post hoc analysis is that only a subset of possible imputation rules has been explored.
To tackle the problem of imputation, AlphaImpute combines long-range phasing, haplotype library imputation, simple phasing and imputation rules, and segregation analysis.
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Our imputation rule for subjects with missing data on these variables was to use the sample mean of subjects with non-missing data for the particular variable.
For the week 104 analysis, patients who entered early escape were included with their originally randomised group without the early escape imputation rule applied.
The Little and Yau "return to baseline" imputation rule, in which any gains over baseline levels dissipate upon dropout, will be used for primary analyses.
Third, for data related to the number of doses missed, the following imputation rule was applied: for respondents answering 'no' to the question "did you miss at least one injection?", but not completing answers for the number of injections missed during each of the three 4-week periods, it was assumed that the first answer was correct (i.e. zero injections were missed).
Coefficient estimates and standard errors were constructed using usual multiple imputation combination rules [ 51], and compared the fit of the models constructed using the imputed data sets with the models fit on the complete-case data.
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