specification of linear model and log transformation in ballgown

Question

[amy16]

Hi, I am following the 'new tuxedo' protocol for my RNA-seq data analysis for Differential gene expression analysis. My experimental design includes 4 varieties, each with control and treatment. I aim to study the varietal effects and the treatment effect. Does the stattest function which includes the linear model, log transformation or does it have to be specified by the user, if so using which function in the ballgown?

Thanks