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iblacksand / WebGestaltR

R package for WebGestalt
https://iblacksand.github.io/WebGestaltR/
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ORA not showing all enriched pathways #1

Closed iblacksand closed 9 months ago

iblacksand commented 9 months ago

Running the same analysis with the R and Rust version have different results. The R version has 60 enriched pathways, while the Rust version has 58. One missing pathway is hsa05167. The rust library outputs the pathway with the right values, but it does not show in the HTML report.

The results from the rust library are below:

    geneSet                                              link size        FDR
39 hsa05167 http://www.kegg.jp/kegg-bin/show_pathway?hsa05167  171 0.01237842
        pValue   expect enrichmentRatio overlap
39 0.001479768 8.993471        2.112644      19

These match the values from the R package. There may be some change made for metabolomics that is causing this and another pathway to not show up in the final report.

Download the files used here: necessaryFiles.tar.gz

iblacksand commented 9 months ago

After some investigation, the sets that are missing are actually hsa04540 and hsa04022. These sets have an FDR of 0.04754 and 0.04923. The rust FDRs have always been a bit higher, so it is likely that the Rust library calculates the FDR as being above 0.05, causing those sets to be ignored.

However, this doesn't explain why not all of the sets are shown in the final HTML, but the same thing occurs in the R package, so this is not due to the Rust library.

iblacksand commented 9 months ago

See #2 for fix