fmath error in clusterProfiler package
I tried to do Gene set enrichment analysis but I encountered the following error message: library(clusterProfiler)
genelist <- read.table("Data/DE-geneSymbol.txt", header = TRUE, stringsAsFactors = FALSE)
head(genelist)
KEGGGeneID GeneSymbol NCBI
1 hsa:3831 KLC1 3831
2 hsa:11274 USP18 11274
3 hsa:81614 NIPA2 81614
4 hsa:5813 PURA 5813
5 hsa:1349 COX7B 1349
6 hsa:7155 TOP2B 7155
genelist <- genelist[,3]
genelist = sort(genelist, decreasing = TRUE)
head(genelist)
[1] 729515 402055 285527 259197 254102 253980
keggGSEA <- gseKEGG(genelist,organism = "hsa", keyType = "kegg",
exponent = 1, nPerm = 1000, minGSSize = 10, maxGSSize = 500,
pvalueCutoff = 0.05, pAdjustMethod = "BH", verbose = TRUE,
use_internal_data = FALSE, seed = FALSE)
preparing geneSet collections...
GSEA analysis...
**Error in fmatch(p, names(stats)) : attempt to set an attribute on NULL**
Could you please help me?
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maleknias •
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Dear all
I solved it. First I prepare my geneList by:
https://github.com/GuangchuangYu/DOSE/wiki/how-to-prepare-your-own-geneList
So the error removed!!
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Dear WouterDeCoster; Thanks a lot!