What measure should be used to calculate fold-change while using Ballgown to compare D.E genes between 2 conditions?

Question

[nancy]

We would like to determine differentially expressed genes between two conditions. We are trying to use the Pertea et al pipeline (Hisat2+Stringtie+Ballgown). Following questions:

1. should the fold change be computed using the fpkm measure or any other?
2. If we use libadjust=FALSE, are the fold-changes simply derived arithmetically from fpkms or is there further normalization involved?

Thanks