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b2slab / FELLA

FELLA: an R package for Metabolomics data enrichment through diffusion
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how to correct for multiple testing with p.scores using diffusion method #19

Closed mingwhy closed 2 years ago

mingwhy commented 2 years ago

Hello,

Thank you for this amazing tool!

I'm using your R package 'FELLA' to perform pathway enrichment analysis. I have a question for the p scores generated using the function runDiffusion. I saw there is a p.score for each pathway, module, enzyme, reaction, and compound. In my case, my metabolome data was generated from fruit flies, there are 10558 pathway/module/enzyme/reaction/compound items, or p.scores.

I guess the p score is analogous to p value? There were 740 p.scores smaller than 0.05. Then if I apply multiple-testing correction using the p.adjust() function in R, none of the corrected 10558 p.scores was smaller than 0.05.

I wonder if I understand the p.score correctly, and do you have any suggestions for multiple-testing correction on those p scores? Thank you so much! All the best! Ming

SergiPicart commented 2 years ago

Dear Ming, The short answer is FELLA's p.scores are not corrected for multiple testing and not used as p-values, but as a statistically adjusted prioritiser. Please find a more detailed discussion on this topic in the Bioc forum: https://support.bioconductor.org/p/9140352

Thank you for your interest in FELLA!