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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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Robust Aitchison PCA? #1450

Open lyoon6 opened 3 years ago

lyoon6 commented 3 years ago

Hello,

Is there a way to perform Robust Aitchison PCA with this package in R? (See implementation in qiime2 here: https://library.qiime2.org/plugins/deicode/19/)

Thanks.

spholmes commented 3 years ago

Hi, Since the transformations are monotone, any rank based transformation is equivalent, and the the way to do a PCA on ranks is developed in detail in the paper here: https://f1000research.com/articles/5-1492 Section : PCA on ranks (the added advantage is you can set a tie threshold, so you are not overinterpreting noise at the low end).

Best wishes Susan

On Tue, Mar 16, 2021 at 9:37 PM lyoon6 @.***> wrote:

Hello,

Is there a way to perform Robust Aitchison PCA with this package in R? (See implementation in qiime2 here: https://library.qiime2.org/plugins/deicode/19/)

Thanks.

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-- Susan Holmes John Henry Samter Fellow in Undergraduate Education Professor, Statistics 2017-2018 CASBS Fellow, Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/