search

MiriamRiquelmeP / DEVEA

an interactive shiny application for Differential Expression analysis, data Visualization and Enrichment Analysis of transcriptomics data
Apache License 2.0
5 stars 1 forks source link

question regarding enrichment #1

Open pbaCamille opened 10 months ago

pbaCamille commented 10 months ago

Hello, I am actually trying your nice shiny app for DEG post analysis. I have a question about enrichment analysis, correct me if i am wrong, but it seems that you didn't use clusterProfiler to compute this approach. I have slightly different results between clusterProfiler and your enrichment analysis, and I would like to understand why. May be you used an other tool or you have a reference paper ? Thanks

MiriamRiquelmeP commented 9 months ago

Dear Camille,

Thanks for using DEVEA and for raising this question.

In order to get the list of significant enriched terms on the enrichment analysis part, DEVEA is indeed using 2 custom functions from 'goana' and 'kegga' functions, included in limma package. This strategy may share some differences on the manner to calculate the stats on the enriched pathways than ClusterProfiler functions, and that could explain the mismatch between DEVEA and your external approach. ClusterProfiler package, among others, is then used for DEVEA to generate the visuals on the final data.frame extracted from our 'customGO' and 'customKegg' functions (based as I mentioned on 'goana' and 'kegga' functions respectively).

Hope this can clarify your issue!

best, M