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datapplab / gage

Generally Applicable Gene-set Enrichment for Pathway Analysis
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FDR cutoff? #4

Open marwa38 opened 1 year ago

marwa38 commented 1 year ago

Hi guys Do you recommend running gage on a FDR cutoff or differentially expressed genes? thanks Marwa

raw937 commented 1 year ago

Depends on the dataset or type. What type of data is it? If RNAseq I would recommend a negative binomial model like DESeq2. If proteomics with spectral counts an initial FDR followed by negative binomial model like DESeq2.