I have been working on an RNA-Seq dataset on which I applied RUVSeq (ruvr method) at the gene-count level to account for some unexpected variance before running DESeq2. I am also working on using DEXSeq to look at differential exon usage. Optimally, I would be able to also apply RUVSeq to the binned exon counts, so that both gene and exon level counts would have been processed similarly. However, I'm not sure if it's appropriate to do this at the exon level- any ideas?
Both of these packages (RUVSeq and of course DESeq2) are BioConductor packages.
(Note: also posted to the Bioconductor board, but did not yet receive a response)