I'm trying to assess the significance of the overlap between groups of genes.
To do this I need the number of genes 'expressed' in my samples - I've read people use an FPKM value >1 as a rough cutoff for this, which gives me 10-12,000 genes depending on the sample.
Does anyone know an equivalent cutoff using the baseMean output from DESeq2? I'm trying to keep number of 'expressed genes' consistent with the analysis it derives from.
Thanks very much!