Minimum size of input genes list and number of samples for fgsea
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4 months ago

I have log2 fold changes from a microarray experiment in which the expression of 768 genes were measured in two groups of patients. Both groups only have 4 patients in them. Additionally, the specific gene expression assay used was the NanoString nCounter Metabolic Pathways Panel. I was wondering if it's ok to run fgsea with this data, even though it's from a small number of patients and only a (relatively) small number of genes were measured, all related to metabolism. I recognize that I'll probably miss enriched gene sets that are not related to metabolism, but in terms of detecting enriched gene sets related to metabolism, will the analysis still work?

gsea fgsea • 131 views
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