Hello everyone,

I wanted to know how to computationally use TMM normalization (typically used with edgeR) with DESeq2. I've read that it's possible to do so. In my analyses, I've always used tximport initially, DESeq (ddTxi), and then worked on the results of DEG. To use TMM normalization, what do I need to convert? Would an approach similar to this work:

```
N <- colSums(geneCount) (vector of library sizes)
tmm.counts <- Ntmm/exp(mean(log(Ntmm))).
```

But in my case, since I don't use edgeR, what would geneCount be? Perhaps `txi$counts`

?

Thank you very much for any advice and help.

Thanks for your response, but What I'm missing is precisely the norm.factor. Do I need to execute this to obtain the norm.factor?

and then proceed with what you confirmed with what I was thinking?

Yes, or the newer version of the function called

`normLibSizes()`

.