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?

You don't have to do any normalization per se. From the help for stattest:

Library size adjustment is performed by default by using the sum of the log nonzero expression measurements for each sample, up to the 75th percentile of those measurements. This adjustment can be disabled by setting libadjust=FALSE. You can use mod and mod0 to specify alternative library size adjustments