Question: CluserProfiler message "No gene can be mapped"
0
gravatar for ARich
13 months ago by
ARich60
United States
ARich60 wrote:

Hi Biostar users,

I am working with clusterprofiler enrichKegg function

KEGG_all = enrichKEGG(regulated.gene$entrez, organism="human")

I have used library(org.Hs.eg.db) to convert gene names(Symbols) to Entrez ID which is the possible input to use this function.

However I am seeing strange message and I am not sure what could be the reason?

--> No gene can be mapped....
--> Expected input gene ID: 7364,127,574537,5538,4351,221
--> return NULL...

Does this means the IDs I am providing have no pathways associated? In that case its not correct because entrez ids I am using have pathways associated except few which don't have are listed as NA.

names=c("57801","2152","54873","7412","148867","1435","90874","NA","2702","NA","1520,","3371","7185","26468","286336","NA","22829")

Due to this I am unable to understand why this message is displayed?

Looking forward for some help.

R • 1.6k views
ADD COMMENTlink modified 4 months ago by zx87547.1k • written 13 months ago by ARich60
2

Are you sure those entrez ID's are for human genes? I checked a few and none seemed to be human proteins.

ADD REPLYlink modified 13 months ago • written 13 months ago by genomax65k

I am quite sure. The reason is because I cant ever find these IDs in my file. --> No gene can be mapped.... --> Expected input gene ID: 7364,127,574537,5538,4351,221 --> return NULL... I used standard conversion from of Symbols to Entrez ids. res$symbol = mapIds(org.Hs.eg.db, keys=row.names(res), column="SYMBOL", keytype="ENSEMBL", multiVals="first")

res$entrez = mapIds(org.Hs.eg.db, keys=row.names(res), column="ENTREZID", keytype="ENSEMBL", multiVals="first"

res$name = mapIds(org.Hs.eg.db, keys=row.names(res), column="GENENAME", keytype="ENSEMBL", multiVals="first")

Which one you checked? the one where its No gene can be mapped?

Thanks

ADD REPLYlink modified 13 months ago • written 13 months ago by ARich60

https://www.ncbi.nlm.nih.gov/protein/7364
https://www.ncbi.nlm.nih.gov/protein/5538

Other ID's in the list above seem to be nucleotide ID's.

ADD REPLYlink written 13 months ago by genomax65k

Hello,

I am also using same function enrichKEGG. Can you please explain how problem was resolved for error

>kegg_enrich <-enrichKEGG(gene = names(log_counts, org = 'uma')
"No gene can be mapped....
--> Expected input gene ID: UMAG_02115,UMAG_00118,UMAG_03692,UMAG_11744,UMAG_02508,UMAG_06105
--> return NULL
ADD REPLYlink modified 7 months ago by genomax65k • written 7 months ago by sbb10
0
gravatar for ARich
13 months ago by
ARich60
United States
ARich60 wrote:

I got the answer to my problem. I was using some cutoff. After the cutoff few comparison had no genes left for down-regulated list This was kind of warning message more that a error.

ADD COMMENTlink written 13 months ago by ARich60
0
gravatar for wangchangliang0209
4 months ago by
wangchangliang02090 wrote:

Hi sbbinfo,

I found that there is something wrong with the help document of enrichKEGG. The "gene" parameter is not Entrez gene ID for other organisms (not "hsa"). For "uma", you should input a vector in "UMAG_02115, UMAG_00118" format, not Entrez gene ID vector.

Best wishes.

ADD COMMENTlink written 4 months ago by wangchangliang02090
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