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PLINK: No difference in quantitative association tests in spite of different disease groups?

Greetings everyone,

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.

plink snp association
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written by spela.salamon • spela.salamon

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