There is a growing body of literature that describes why RPKM/FPKM is not the most optimal solution when wanting to conduct differential expression analysis (see e.g. Dillies, M.A., Brief. Bioinf., 2012 and Soneson & Delorenzi, 2013). There's also a video from Lior Pachter (, one of the FPKM author that explains why. For that reason I state in the vignette of easyRNASeq that RPKM should only be use for visualisation if at all. In the upcoming release of easyRNASeq, I will disable RPKM altogether.
The best approach is to get the unmodified not-normalized count table from easyRNASeq and use that for edgeR.
If you really want to compute your FPKM, you can get the gene length from your annotation (your gff3 or retrieve it from biomaRt) and provide it as a named vector to the function. If you do not have an easy mean to extract the gene length, you can run easyRNASeq with outputFormat="RNAseq". This will return you an object of class RNAseq and you can access your annotation by accessing the genomicAnnotation slot (using the genomicAnnotation accessor) or if you computed geneModels, using the geneModel slot. Note that possibly a number of these functions may not be exported by the easyRNASeq package and you need to prepend the function name with easyRNASeq:: if you want to access them.