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Question: deseq2 pseudo counts
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gravatar for Prasad Siddavatam
3.5 years ago by
United States
Prasad Siddavatam150 wrote:

For each sample (and replicate), do I have to convert zero read counts to ones (pseudo counts) while running deseq2?

I assume I don’t have to, but a quick clarification.

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Prasad Siddavatam150
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gravatar for Michael Love
3.5 years ago by
Michael Love17k
United States
Michael Love17k wrote:
Hi Prasad, No you don't have to convert. The zeros (including when all samples have a zero), are automatically handled by the model (and by the software).
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Michael Love17k

 

Hello, Michael!

How exactly does DESeq2 handles with the zero counts? I tried to understand and look for it but is still unclear for me. Thanks

 

ADD REPLYlink modified 3 months ago • written 3 months ago by mgdias.jose0

Here is the DESeq2 paper with details on the methods:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302049/

Counts of zero are not treated differently by the statistical model than a count of 1, 2, ...

ADD REPLYlink written 3 months ago by Michael Love17k
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gravatar for Prasad Siddavatam
3.5 years ago by
United States
Prasad Siddavatam150 wrote:

Thank you very much.

ADD COMMENTlink written 3.5 years ago by Prasad Siddavatam150
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