pathway analysis on FDR?

BaderLab / Cytoscape_workflows

collection of notebooks with different cytoscape workflows

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pathway analysis on FDR? #8

Open marwa38 opened 1 year ago

marwa38 commented 1 year ago

HI guys It is not an issue it a question regarding enrichmenet analysis. Do you recommend running pathway analysis without FDR cutt-off so it is independent of DGE genes?

I am a bit new to rnaseq so your comments are helpful. M

risserlin commented 1 year ago

We recommend pathway analysis on a ranked unthresholded list if possible with your dataset. Please see - https://www.nature.com/articles/s41596-018-0103-9 for the details.