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neurorestore / DE-analysis

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Question about DESeq2 settings #3

Open CarlottaHS opened 2 years ago

CarlottaHS commented 2 years ago

Hi,

thank you for providing the code for your analysis! I was using your function PseudobulkDE to analyze my data and looked to your default setting of DESeq2 as I have used DESeq2 myself before on pseudobulk data. What is the reasoning behind setting independentFiltering=FALSE in the results() function of DESeq2. I would be very curious to hear your thoughts on that as I have seen our results differ mostly due to this.

Thanks again for this code!

skinnider commented 2 years ago

Hi @CarlottaHS - the motivation was that in our benchmark, in order to effect a fair comparison between statistical methods, they needed to be compared on the same set of genes. The simplest way to do this was to disable filtering for all methods. Our Libra package inherits this decision, mostly because we didn't really think too much about it when packaging up the code in this repository, but in general I think it's definitely a reasonable analytical decision to enable independentFiltering.