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Question: deseq2 pseudo counts
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gravatar for Prasad Siddavatam
2.5 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 2.5 years ago • written 2.5 years ago by Prasad Siddavatam150
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gravatar for Michael Love
2.5 years ago by
Michael Love12k
United States
Michael Love12k 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 2.5 years ago • written 2.5 years ago by Michael Love12k
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gravatar for Prasad Siddavatam
2.5 years ago by
United States
Prasad Siddavatam150 wrote:

Thank you very much.

ADD COMMENTlink written 2.5 years ago by Prasad Siddavatam150
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