Hi all, How would you use the ballgown package in conjunction with voom, edgeR, DESeq, limma?
The bioarXiv paper seems to be making the claim that ballgown gaps the bridge between cufflinks and tools like Limma, Voom, edgeR, DEseq.
I don’t understand how voom, edgeR and DEseq can by used at the gene or transcript level, since these require raw counts , which ballgown/cufflinks do not return (unlike estimates from RSEM or Sailfish for instance). That is unless one is ready to feed FPKM values to voom(), but that looks incorrect to me.
As for Limma or the ballgown model, one has to accept working on the log2(1+FPKM) scale. But then one wonders why using ballgown in the first place when we can just parse the output of cuffnorm and feed those into Limma.