FDR cutoff?

[marwa38]

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

[raw937]

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.