Question: Appropriate to apply RUVSeq to exon bin counts for DEXSeq?
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gravatar for Adamc
2.1 years ago by
Adamc570
United States
Adamc570 wrote:

Hi,

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.

Thanks!

(Note: also posted to the Bioconductor board, but did not yet receive a response)

ADD COMMENTlink written 2.1 years ago by Adamc570

I'm having similar issues. Did you ever find an answer for your question?

ADD REPLYlink written 7 weeks ago by unawaz40
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