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biocore / DEICODE

Robust Aitchison PCA from sparse count data
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Fixes the centering issue #38

Closed mortonjt closed 5 years ago

mortonjt commented 5 years ago

This looks like it'll fix the centering issue. Below is proof with the metabolomics data

image

We still need

cameronmartino commented 5 years ago

@mortonjt looks like the test expected output needs to be updated with the new centering for the standalone and q2 tests.

mortonjt commented 5 years ago

ok, @cameronmartino . Fixed the standalone tests. I'm at a bit of a loss on how to fix the q2 tests, thoughts?

cameronmartino commented 5 years ago

@mortonjt it seems to be passing. Not sure why 0e1b445 failed?

mortonjt commented 5 years ago

Maybe we don't need that assert statement anymore - I bet the sign issue is resolved with the SVD postprocessing step

cameronmartino commented 5 years ago

@mortonjt agreed!

mortonjt commented 5 years ago

fyi - the percentages look a little weird. otherwise, this should be good to go

cameronmartino commented 5 years ago

@mortonjt the percentages look okay too me? The centering is so much better (look at those metabolites)

microbes

emperor_microbes

metabolites

emperor_metabolites

mortonjt commented 5 years ago

Yeah, this looks reasonable to me

On Tue, Jul 2, 2019, 12:43 PM Cameron Martino notifications@github.com wrote:

@mortonjt https://github.com/mortonjt the percentages look okay too me? The centering is so much better (look at those metabolites) microbes

[image: emperor_microbes] https://user-images.githubusercontent.com/15164295/60537994-904a0480-9cbe-11e9-9f0d-d998e35a3f42.png metabolites

[image: emperor_metabolites] https://user-images.githubusercontent.com/15164295/60537995-904a0480-9cbe-11e9-94b9-54ef3ea17fc5.png

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