What measure should be used to calculate fold-change while using Ballgown to compare D.E genes between 2 conditions?
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4.9 years ago
nancy ▴ 90

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

RNA-Seq Hisat2 Ballgown Stringtie • 1.4k views
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