I have been using (and really digging) PLINK for a while now, but there is a problem i can't seem to get around.
I am trying to perform an association analysis with individuals of three and not two different affection statuses. Since affection status can only be set to 2 or 1 in PLINK (affected vs. unaffected), i have made two different PED files with one or the other having one of the affected groups' status set to 0 (missing), controls always being set to 1.
I would now like to perform an association analysis with a quantitative trait, which i have placed in the PHENO file. All good, but regardless of which file i select (PED1 or PED2), the results are the same, indicating something is not right.
PLINK correctly reports the numbers of cases, controls and missing in each of the the cases.