some genes have the same rank Foldchange

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Warning message in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, :
“There are ties in the preranked stats (23.03% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.”

Warning message in fgseaMultilevel(...):
“There were 1171 pathways for which P-values were not calculated properly due to unbalanced (positive and negative) gene-level statistic values. For such pathways pval, padj, NES, log2err are set to NA. You can try to increase the value of the argument nPermSimple (for example set it nPermSimple = 100000)”

Warning message in fgseaMultilevel(...):
“For some of the pathways the P-values were likely overestimated. For such pathways log2err is set to NA.”

Warning message in fgseaMultilevel(...):
“For some pathways, in reality P-values are less than 1e-10. You can set the `eps` argument to zero for better estimation.”
leading edge analysis...

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