Error in GSEA function of clusterProfiler on R

Question

[j.thomas93]

I am trying to run GSEA on RStudio using this:

library(clusterProfiler)
library(enrichplot)


# SET THE DESIRED ORGANISM HERE
organism = "org.Hs.eg.db"
library(organism, character.only = TRUE)

# reading in data from deseq2
df = read.csv("expression_set_full-gsea.csv", header=TRUE)

# we want the log2 fold change 
original_gene_list <- df$logFC

# name the vector
names(original_gene_list) <- df$X

# omit any NA values 
gene_list<-na.omit(original_gene_list)
write.csv(df, file ="dfff.csv")


# sort the list in decreasing order (required for clusterProfiler)
gene_list = sort(gene_list, decreasing = TRUE)
gse <- gseGO(geneList=gene_list, 
             ont ="ALL", 
             keyType = "ENSEMBL", 
             nPerm = 10000, 
             minGSSize = 3, 
             maxGSSize = 800, 
             pvalueCutoff = 0.05, 
             verbose = TRUE, 
             OrgDb = organism, 
             pAdjustMethod = "none")

But i keep getting the following error:

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘species’ for signature ‘"character"’
In addition: Warning messages:
1: In .GSEA(geneList = geneList, exponent = exponent, minGSSize = minGSSize,  :
  We do not recommend using nPerm parameter incurrent and future releases
2: In fgsea(pathways = geneSets, stats = geneList, nperm = nPerm, minSize = minGSSize,  :
  You 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.
3: In serialize(data, node$con) :
  'package:stats' may not be available when loading
4: In serialize(data, node$con) :
  'package:stats' may not be available when loading

Any idea what is happening here and how can I fix it. The "In addition" warnings are non fatal, but the error before obviously stops the function.

Thanks in advance!

Answer 1

[jared.andrews07]

You aren't passing the OrgDb parameter properly. It has to be an actual OrgDb object, rather than the string associated with it. So that parameter should be OrgDb = org.Hs.eg.db rather than a character variable for "org.Hs.eg.db".

[j.thomas93]

Yup! Of course, I wws bashing my head against a wall for hours with that!

Thanks for your help!

[MaxF]

I'd like to use the clusterProfiler function in a pipeline. Is it possible to enter the orgdb as a variable?

[jared.andrews07]

Sure. xx <- org.Hs.eg.db. If you're asking how to evaluate a string as an expression or whatever, see this stackoverflow question for options.