I am running associations in Plink and I have a covariate variable that I would like to correct for which codes for 4 different diseases. When I include this covariate as a numeric variable, e.g. 1,2,3,4, Plink works fine. However from the Manual it seems that categorical variables should be recoded as binary dummy variables, e.g. 0/1 for disease 1; 0/1 for disease 2, and so on. But when I do that, Plink gives me NA results. Maybe because of small variation in the phenotypes... My question is, how do these two methods differ? Is it ok for me to use the numeric variable instead?
Thank you for any advice.