Robust Aitchison PCA?

[lyoon6]

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]

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. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1450>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJFZPOBWFVOVGTBQF5FZA3TEAWZJANCNFSM4ZJ2YWLQ> .

-- 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/