How to normalise data in ballgown?
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?
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lakshmi9c •
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Cross-posted: https://support.bioconductor.org/p/133647/
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/DEseq2protocol