Question: CluserProfiler message "No gene can be mapped"
0
gravatar for ARich
10 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 • 1.2k views
ADD COMMENTlink modified 5 weeks ago by zx87546.2k • written 10 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 10 months ago • written 10 months ago by genomax60k

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 10 months ago • written 10 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 10 months ago by genomax60k

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 4 months ago by genomax60k • written 4 months ago by sbbinfo10
0
gravatar for ARich
10 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 10 months ago by ARich60
0
gravatar for wangchangliang0209
5 weeks 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 5 weeks ago by wangchangliang02090
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 751 users visited in the last hour