Entering edit mode
2.7 years ago
j.thomas93 • 0
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!
Yup! Of course, I wws bashing my head against a wall for hours with that!
Thanks for your help!
I'd like to use the clusterProfiler function in a pipeline. Is it possible to enter the orgdb as a variable?
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.