How to normalise data in ballgown?

Question

[lakshmi9c]

Hi, I am working on a RNA-Seq project in ballgown to find differentially expressed genes between two groups. I have loaded the ballgown objects in R and need to normalise the data before DGE analysis. I tried calcNormFactors() using edgeR, but that needs matrix input, instead I have a ballgown object. Could you please guide me on how to normalise the data from ballgown using R functions?

[Kevin Blighe]

Cross-posted: https://support.bioconductor.org/p/133647/

[cpad0112]

My understanding is that ballgown works with FPKMs (RPKMs) and these values are already normalized (as I understand). If you are comfortable, use alignment (hisat2/star/etc) -> featurecounts -> edgeR/DEseq2 protocol