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FAQ
Q1: ssGSEA missing p value and FDR?
A: The original ssGSEA alogrithm will not give you pval or FDR, so, please ignore the gseaplot generated by ssgsea. It's useless and misleading, therefore, fdr, and pval are not shown on the plot. If you'er seeking for ssGSEA with p-value output, please see here: https://github.com/broadinstitute/ssGSEA2.0
Actually, ssGSEA2.0 use the same method with GSEApy to calculate P-value, but FDR is not.
Q2: How to save plots using gseaplot, barplot, dotplot,heatmap in Jupyter?
A: e.g. gseaplot(...ofname='your.plot.pdf'). That's it
Q3: I want to use python 2 version of GSEApy.
A: Not recommended. I'll not fix the bugs in py2 version. But if you need, install v0.9.4 and see the docs here: https://gseapy.readthedocs.io/en/v0.9.4/index.html.
Q4: What cutoff mean in functions, like enrichr(), dotplot,barplot ?
A: This argument control the terms (e.g FDR < 0.05) that will be shown on figures, not the result table ouput.