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tbaccata / amica

amica: an interactive and user-friendly web-based platform for the analysis of proteomics data
GNU General Public License v3.0
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New Feature Request - Statistics with Xiao Correction #12

Closed Maithy15 closed 2 years ago

Maithy15 commented 2 years ago

Hi Sebastian,

Is it possible to implement another significant cutoff other than the ones available? It is called Xiao correction. Here is the link to the paper. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957066/

Thanks Maithy

tbaccata commented 2 years ago

Hi Maithy,

with the global parameters in the Differential abundance tab you can already account for log2FC and (adj.) p-value thresholds. A combined signficance cutoff (e.g -log10(p-value) * log2FC) is reasonable, when applied to a rank a list of genes for gene set enrichment analysis (GSEA), where you would usually consider all genes (DE or not DE).

amica's query interface was designed to provide user defined thresholds to retrieve a list of diff. abundant proteins, and then to apply subsequent analysis (e.g over-representation analysis) and visualizations on that list. I don't see any improvement in a combined significance value for amica's functionality (for example, I'd have a more difficult time defining common, reasonable combined score cutoffs compared to the common filtering by significance and log2FC), I think the implemented thresholds are sufficient.

Best, Sebastian