2.2 years ago by

Philadelphia, PA

A logistic regression is where your dependent, outcome variable is dichotomous or binary (aka logical).

GAPIT is a mixed model linear regression, which means it tries to divide the regressors into fixed and random effects. This is super important in agriculture where most of all the GWAS signals end up being SNPs associated with some inbred line.

They correct for this by this assigning fixed effects to SNPs and call the population a random effect, or vice-versa.

GAPIT assumes a continuous linear outcome variable. There is such a thing as mixed model logistic regression. Actually, I wouldn't be surprised if GAPIT has a logistic method hiding somewhere.

So...is your outcome a number or a category?