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Zhuoqing Fang edited this page May 2, 2020 · 19 revisions

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.

Q: What Enrichr database are supported?

A: Support modEnrich (https://amp.pharm.mssm.edu/modEnrichr/) . Now, Human, Mouse, Fly, Yeast, Worm, Fish are all supported.

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

Q: How to use Yeast database in gseapy.enrichr()?

Because some library names are the same in different Enrichr database , you have to set an additional augment organism when use database other than Human

gss = gseapy.get_library_name('Yeast')
enr = gseapy.enrichr(gene_list=...,
                     gene_sets=gss, 
                     organism='Yeast',# don't forget to set organism="Yeast"
                     ...)

Outputs

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

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

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.

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