Hello,

I am trying to perform enrichment analysis using custom annotations. I have a gene list of symbols and a TERM2GENE which is a dataframe where the first column is the custom annotation ID and the second column is the associated gene in symbol format. I also have a TERM2NAME file which is the annotation ID and a descriptor. I had assumed that the format of the gene ID (entrezID vs. gene symbol) wouldn't matter since I am supplying the TERM2GENE list in the same format. However, when I try to run this I get the following error. I have also tried converting the symbol to entrezID, just to make sure that wasn't the problem, and get the same error.

--> No gene can be mapped.... --> Expected input gene ID: fbxw11a,cebpa,nos2a,ndel1b,ndel1a,caspa --> return NULL...

Any help would be greatly appreciated.

Code should be placed in three backticks as shown below

Example truncated code

GeneList <- data.frame(geneID = c("a2ml","abcb6a", "abcb7", "abi3bpb"))

T2G -> data.frame(TermID = c("ZFA:0000084", "ZFA:0001399", "ZFA:0000114", "ZFA:0000124"), geneID = c("a2ml","abcb6a", "abcb7", "abi3bpb"))

result -> enricher(GeneList, TERM2GENE = T2G)



# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )

The argument (content) used for gene should be a (character) vector, but yours is a data.frame.

Upon fixing that, it works... the error that is appearing now is to be expected.

> library(clusterProfiler)
> 
> GeneList <- data.frame(geneID = c("a2ml","abcb6a", "abcb7", "abi3bpb"))
> 
> T2G <- data.frame(TermID = c("ZFA:0000084", "ZFA:0001399", "ZFA:0000114", "ZFA:0000124"), geneID = c("a2ml","abcb6a", "abcb7", "abi3bpb"))
> 
> result <- enricher(gene = GeneList, TERM2GENE = T2G)
--> No gene can be mapped....
--> Expected input gene ID: a2ml,abcb7,abi3bpb,abcb6a
--> return NULL...
> 
> class(GeneList)
[1] "data.frame"
> 
> class(GeneList$geneID)
[1] "character"
> 
> result <- enricher(GeneList$geneID, TERM2GENE = T2G)
No gene sets have size between 10 and 500 ...
--> return NULL...
>