GSEA analysis error: unable to find an inherited method for function ‘species’ for signature ‘"character"’

Question

[Jin]

Dear everyone,

I an trying to use gseGO to do GSEA analysis,while when I run my code, there turns to be an error which really make me confused, so I hope that your advises will help me, thanks in advance:

Here I paste my code:

# this is the libs I loaded:
library(dplyr)
library(tibble)
library(openxlsx)
library(ggplot2)
library(ComplexHeatmap)
library(clusterProfiler)
library(org.Hs.eg.db)
library(AnnotationDbi)
library(enrichplot)
library(survival)
library(survminer)

gseaGO <- gseGO(geneList     = gene_list,
                    ont      = 'BP',
                    OrgDb = "org.Hs.eg.db",
                    nPerm        = 1000,
                    minGSSize    = 10,
                    pvalueCutoff = 0.2,
                    verbose      = FALSE)

Here is the error instruction:

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘species’ for signature ‘"character"’ We do not recommend using nPerm parameter incurrent and future releasesYou are trying to run fgseaSimple. It is recommended to use fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument in the fgsea function call.There are ties in the preranked stats (16.85% of the list). The order of those tied genes will be arbitrary, which may produce unexpected results.Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘species’ for signature ‘"character"’

Thank you for help !

[Hamid Ghaedi]

Please use Code Sample option to indicate the code in your post. If you like, check this tutorial, it can help you to understand the steps you needed to go through.