Question: CluserProfiler message "No gene can be mapped"
0
gravatar for ARich
17 months ago by
ARich80
United States
ARich80 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 • 2.3k views
ADD COMMENTlink modified 8 months ago by zx87547.9k • written 17 months ago by ARich80
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 17 months ago • written 17 months ago by genomax70k

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 17 months ago • written 17 months ago by ARich80

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 17 months ago by genomax70k

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 11 months ago by genomax70k • written 11 months ago by sbb10
0
gravatar for ARich
17 months ago by
ARich80
United States
ARich80 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 17 months ago by ARich80
0
gravatar for wangchangliang0209
8 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 8 months 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: 1547 users visited in the last hour