Why the results are different between R and GSEApy

[sinorockie]

In R language
library(GSVA) library(GSVAdata) params <- ssgseaParam(exprData = exp4, geneSets = genesets) gsva_results <- gsva(params)
In GSEpy
ssgsea_kwargs = { "min_size": 1, "max_size": exp4.shape[0], "weight": 0.25, "verbose": True, "seed": 1 } ss = gseapy.ssgsea(data=data, gene_sets=gene_sets, **ssgsea_kwargs) gsva_results = ss.res2d.pivot(index='Term', columns='Name', values='NES')

I'm trying to reproduce the result in GSEApy, however, the result is different from the result from R, I have check the input data and genesets which are same.

Is there any one can tell me the reason?

[zqfang]

I think there are some filtering steps before real calculation.

see here for testing codes. if you use the same input files for both gseapy and GSVA. They have the same output