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FAQ
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.
A: In short,
- prerank is used for comparing two group of samples (e.g. control and treatment), where the gene ranking are defined by your custom rank method (like t-statistic, signal-to-noise, et.al).
- ssGSEA is used for comparing individual samples to the rest of all, trying to find the gene signatures which samples shared the same (use ssGSEA when you have a lot of samples).
The statistic between prerank (GSEA) and ssGSEA are different.
Assume that we have calculated each running enrichment score
of your ranked input genes, then
- es for GSEA:
max(running enrichment scores)
ormin(running enrichment scores)
- es for ssGSEA:
sum(running enrichment scores)
A: Support modEnrich (https://amp.pharm.mssm.edu/modEnrichr/) . Now, Human, Mouse, Fly, Yeast, Worm, Fish are all supported.
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.
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
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"
...)
A: e.g. gseaplot(..., ofname='your.plot.pdf'). That's it
A: This argument control the terms (e.g FDR < 0.05) that will be shown on figures, not the result table output.