Hi,

I'm attempting to use 'enricher' and 'GSEA' functions from clusterprofiler package to analayze gene sets from MSigDB. 

The following is the code I'm using:

​> gmtfile <- "/path/c5.all.v6.1.entrez.gmt"
> c5 <- read.gmt(gmtfile)

> head(df)

   ENTREZID log2FoldChange

1 100516980     0.11587633

2 100155074     0.11587633

> egmt <- enricher(as.character(df[,1]), TERM2GENE=c5)

--> No gene can be mapped....

--> Expected input gene ID: 27433,10846,23479,3669,65977,10808

--> return NULL...

> head(geneList)

100154447    396596 100516171 100155895    397132 100515447

6.035077  4.837211  4.629196  4.524015  4.420449  4.401480

> egmt2 <- GSEA(geneList, TERM2GENE=c5, verbose=FALSE)

--> Expected input gene ID: 54932,23001,3329,2035,9837,22894

Error in check_gene_id(geneList, geneSets) :

  --> No gene can be mapped....

ANSWER: I got a list of pathways by doing the following

eg = bitr(d$SYMBOL, fromType="SYMBOL", toType=c("PATH", "ENTREZID"), OrgDb="org.Ss.eg.db")
> head(eg)
    SYMBOL  PATH  ENTREZID
1    ACKR1 05144 100154447
2     FMO1 00982    397132

tt <- eg[,c(2,3)]
> head(tt)
    PATH  ENTREZID
1  05144 100154447
2  00982    397132

> egmt <- enricher(as.vector(df[,1]), pvalueCutoff=1, qvalueCutoff=1, pAdjustMethod = "BH", TERM2GENE=tt)
> head(egmt)
ID Description GeneRatio BgRatio pvalue p.adjust qvalue
00010 00010       00010   32/2868 32/2868      1        1      1
00020 00020       00020   20/2868 20/2868      1        1      1

I'm not sure why the pathway description aren't displayed. Any suggestions? Thanks 

What’s the organism you want to analyze? according to https://www.ncbi.nlm.nih.gov/gene/100516980, it is Sus scrofa.

I guess the gmtfile <- "/path/c5.all.v6.1.entrez.gmt" is annotation for human.

This is why it throw the msg:

--> No gene can be mapped....  
--> Expected input gene ID: 27433,10846,23479,3669,65977,10808

​