Hello,

I am interested in doing some cross species DEG analysis similar to this post using orthologous genes across two closely related species. For curiosity I wanted to compare the sizefactors with and without the gene length information but when I try to use sizeFactors(dds) for the former case, I get a NULL vector. Is there some documentation on how the size factor is calculated when the gene length is specified?

Thank you very much.

The estimateSizeFactors() function does not use the gene length information at all, see for reference the source code:

https://github.com/thelovelab/DESeq2/blob/devel/R/core.R#L535-L578