FAQ

Questions

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: I want to use python 2 version of GSEApy.

A: Not recommended. Python 2 version has been abandoned since v0.9.4 (No bug fix anymore). If you need, install v0.9.4 and see the docs here: https://gseapy.readthedocs.io/en/v0.9.4/index.html.

Inputs

Q: Use custom defined GMT file input in Jupyter?

A: argument gene_sets accept dict input. This is useful when use your own gene_sets. An example dict looks like this:

gene_sets = {
              "term_1": ["gene_A", "gene_B", ...],
              "term_2": ["gene_B", "gene_C", ...],
               ...
              "term_100": ["gene_A", "gene_T", ...]
             }

APIs support dict input: gsea, prerank, ssgsea, enrichr

Outputs

Q: How to save plots using gseaplot, barplot, dotplot,heatmap in Jupyter?

A: e.g. gseaplot(..., ofname='your.plot.pdf'). That's it

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Q: 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 output.