Question

DESeq2 PCOA Plots

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amgodogma ▴ 10

@amgodogma-12973

Last seen 5.4 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 • 1.3k views

ADD COMMENT • link 5.6 years ago amgodogma ▴ 10

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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

ADD REPLY • link 5.6 years ago amgodogma ▴ 10

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There may be a back-conversion function.

ADD REPLY • link 5.6 years ago Michael Love 43k

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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

ADD REPLY • link 5.6 years ago amgodogma ▴ 10

score 0 · Answer 1 · 2019-04-07

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Michael Love 43k

@mikelove

Last seen 15 hours ago

United States

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

ADD COMMENT • link 5.6 years ago Michael Love 43k