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saezlab / MetaProViz

R-package to perform metabolomics pre-processing, differential metabolite analysis, metabolite clustering and custom visualisations.
https://saezlab.github.io/MetaProViz/
GNU General Public License v3.0
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proDA in MVI or DMA (DMA- missing values) #46

Closed ChristinaSchmidt1 closed 11 months ago

ChristinaSchmidt1 commented 1 year ago

About proDA, if I have understood this correctly, what you describe is actually done as part of the Log2FC calculation. So it is not a MVI as such, but if someone would want to also calculate Log2FC and stats from metabolites where some missing values are present.

Dimitrios:

About proDA yes it sais this: image

So its not really doing imputation here. But here: https://support.bioconductor.org/p/122916/

I undestood that they make the model and then use that model to make a full matrix from one with missing values.

ChristinaSchmidt1 commented 1 year ago

We do not perform statistical testing on metabolites with missing values. We can consider to add a parameter that allows this for samples were X% of the replicates in the condition is detected.

In this regard I was also pointed towards the package proDA (https://www.bioconductor.org/packages/release/bioc/html/proDA.html) for proteomics data, that does MVI as part of the Log2FC calculation. So this is something good to check and see how they have done this.

ChristinaSchmidt1 commented 11 months ago

I will close this issue as i think with adding limma, we already provide a good test that accespts missing values.