Hi Mike,

hope you have a minute to clarify:

I would like to plug in existing size factors into `vst`

like

`sizeFactors(dds) <- edgeR::calcNormFactors(count.matrix)`

and then `vst(dds)`

in order to use the exact same factors I used for DE testing with edgeR.

While technically possible I'd like to know whether the direct output of `calcNormFactors`

is appropriate here. Thanks for your time!

Thanks, makes sense. I get a bit into trouble with the

`less than 'nsub' rows with mean normalized count > 5,`

since the magnitude of the factors from edgeR are completely different than the ones from DESeq2 (much larger with edgeR when multiplying with colSums, maybe try to scale by 1e+06), but this is not DESeq2-specific anymore, therefore won't bother you with it. Will try to figure out sth. that works for me, thanks for your answer!