DESeq2 PCOA Plots
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amgodogma ▴ 10
@amgodogma-12973
Last seen 3.4 years ago

Hi all

I was wondering if anyone had a pipeline for calculating distances by Bray-Curtis and plotting a PCOA plot with a DESeq2 object?

The plotPCA function doesn't seem to give you the option to choose which distance metric to use.

If anyone has any ideas/suggestions that would be very helpful

thanks

deseq2 • 611 views
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HI Michael

Thanks for your response. I know how to do it with a phyloseq object. But for the project I'm working on I have a DESeq2 object.

thanks

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There may be a back-conversion function.

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Sorry I replied to the wrong comment. Yeah does anyone know of a back-conversion function or Is there a way I can calculate the distance matrix within the DESeq object?

thanks

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@mikelove
Last seen 7 hours ago
United States

I think you could get this from phyloseq? Maybe post again and tag that package?

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