Is there a stagewise testing procedure for DESeq2?

Question

[Jay-Run]

I'm trying to perform a differential gene expression analysis in which I want to compare edgeR and DESeq2 methods. I've already done the stagewise testing for edgeR and was wondering if there's a stagewise testing procedure for DESeq2, as well?

Thank you.

Answer 1

[Devon Ryan]

Wouldn't the stageR package enable this for all possible upstream packages (e.g., DESeq2 and edgeR)? They use edgeR in their vignette because one of the authors wrote it, but there's no reason you couldn't use something else to make the input into stageR().

[Jay-Run]

Thank you, Devon.

I read this vignette a while ago in which they performed stage-wise limma-voom and DEXSeq analysis. I'm gonna have another look and see what I'm missing. Happens a lot since I'm at the beginning of the road.

Best,

[Devon Ryan]

If you figure out the steps feel encouraged to post a tutorial with that. I'm sure it'd be quite useful for many folks :)

[Jay-Run]

Of course. I'd be more than happy to share my experience with others.

Thank you.