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wejlab / animalcules

R shiny app for interactive microbiome analysis
https://wejlab.github.io/animalcules-docs/
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Counts file - only relative abundance data #43

Closed davitero closed 3 years ago

davitero commented 3 years ago

Hello, My data are only OTUs and their relative abundances because they were obtained in a previous investigation.

So I was wondering, can I work with my relative abundance data instead of read counts? That is, can I use this information as count file?

wevanjohnson commented 3 years ago

Yes, you can, multiple, your abundances by a large number, say 100000 and then round to the nearest integer, and treat them as counts. You can use any of the functions that use relative abundance just fine. But be careful with anything that uses the counts directly, e.g. DESeq2 on these data.

On Oct 10, 2020, at 12:31 PM, davitero notifications@github.com wrote:

Hello, My data are only OTUs and their relative abundances because they were obtained in a previous investigation.

So I was wondering, can I work with my relative abundance data instead of read counts? That is, can I use this information as count file?

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davitero commented 3 years ago

Dear Evan, Thank you for your answer. I will do as you say. Best, Dave