I've got a dataset with survey data. Since some items are not applicable to every participant, I assigned a user defined missing value (i.e. 990). If an item was applicable for a participant, but was not filled in, then I assigned a user defined missing value of 999 to it. So when running a multiple imputation, I want all 999-values to be included in the imputation (and therefore all 999-values should be replaced by calculated values), but 990-values shouldn't be replaced at all! How could this be done? I am wondering that I've found no answer for this problem although one might assume that this procedure is often requested.
I posted it on stackexchange also.