How to use EnrichGo of Cluster Profiler
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Carolina • 0
@Carolina-24585
Last seen 25 days ago

Could anyone please help me with EnrichGo and barplot using clusterprofiler R package?

The OrgDb should be Salmo salar, but I did not found this in the reference.

enrichGO(gene, OrgDb="org.Dr.eg.db", keyType = "ENTREZID", ont = "BP", pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, qvalueCutoff = 0.2, minGSSize = 10, maxGSSize = 500, readable = FALSE, pool = FALSE)

Results:

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

--> Expected input gene ID: 101885477,566367,567006,572540,768189,30554

--> return NULL...

Please, I appreciate some recommendation for this, because I am starting in these analyses.

Thanks, Carolina

EnrichGO clusterProfiler • 140 views
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Could you share what is the output of head(gene)?

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@james-w-macdonald-5106
Last seen 1 day ago
United States

If you are using Salmo salar NBCI Gene IDs and hoping that you can use an OrgDb that contains NCBI Gene IDs for Danio rerio, then I can assure you that won't work. Just because they are both fish doesn't mean that NCBI gives them the same Gene IDs.

There is an OrgDb for S salar, which you can get from the AnnotationHub

> library(AnnotationHub)
> hub <- AnnotationHub()
  |======================================================================| 100%

snapshotDate(): 2020-10-27

> query(hub, c("salmo salar", "orgdb"))
AnnotationHub with 1 record
# snapshotDate(): 2020-10-27
# names(): AH85416
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Salmo salar
# $rdataclass: OrgDb
# $rdatadateadded: 2020-10-27
# $title: org.Salmo_salar.eg.sqlite
# $description: NCBI gene ID based annotations about Salmo salar
# $taxonomyid: 8030
# $genome: NCBI genomes
# $sourcetype: NCBI/UniProt
# $sourceurl: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, ftp://ftp.uniprot.org/p...
# $sourcesize: NA
# $tags: c("NCBI", "Gene", "Annotation") 
# retrieve record with 'object[["AH85416"]]' 

> ssalar <- hub[["AH85416"]]
downloading 1 resources
retrieving 1 resource
  |======================================================================| 100%

> ssalar
OrgDb object:
| DBSCHEMAVERSION: 2.1
| DBSCHEMA: NOSCHEMA_DB
| ORGANISM: Salmo salar
| SPECIES: Salmo salar
| CENTRALID: GID
| Taxonomy ID: 8030
| Db type: OrgDb
| Supporting package: AnnotationDbi

Please see: help('select') for usage information

Now you will note that the central ID is the GID. Which generally is not the same as the NCBI Gene ID. However, in this case the GID and EntrezGene ID (which is now called the NCBI Gene ID) are the same. Presumably enrichGO is capable of using a 'bare' OrgDb rather than assuming it's installed, but let us know if you have any further problems.

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