Question

Cross-species analysis using DESeq2 - size factor computation

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pl23 • 0

@4b83ad99

Last seen 6 months ago

Canada

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.

dese DESeq2 • 516 views

ADD COMMENT • link 10 months ago • updated 9 months ago pl23 • 0

score 0 · Answer 1 · 2024-01-26

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ATpoint ★ 4.5k

@atpoint-13662

Last seen 4 days ago

Germany

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

ADD COMMENT • link 10 months ago ATpoint ★ 4.5k

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Thanks! My confusion is resolved - the sizeFactors() function is only used for constant normalization factors over genes. To compute normalization factors, I ran dds = DESeq(dds) first and then extracted normalizationFactors(dds).

ADD REPLY • link 9 months ago pl23 • 0