No gene can be mapped in Cluster profiler
1
0
Entering edit mode
Safina • 0
@safina-24123
Last seen 10 months ago

Input file is the list of gene ids along with fold change values:

    14  1.23
    43  -1.18
    52  1.42
    90  -1.2
    212 1.42
    291 -1.11
    337 1.29
    351 -1.31
    358 1.19
    372 -1.5
    411 -1.43
    444 -1.13
    471 -1.24
    585 -1.46
    596 -1.47
    607 -1.47
    632 1.37

Column one is gene id and column 2 is fold change

Code having error is:

ego <- enrichGO(gene          = gene,
                universe      = names(geneList),
                OrgDb         = org.Hs.eg.db,
                ont           = "CC",
                pAdjustMethod = "BH",
                pvalueCutoff  = 0.01,
                qvalueCutoff  = 0.05,
        readable      = TRUE)

Error:

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

--> Expected input gene ID: 10856,8295,25942,345651,79101,51780

--> return NULL...

clusterProfiler • 178 views
ADD COMMENT
0
Entering edit mode
Guido Hooiveld ★ 3.0k
@guido-hooiveld-2020
Last seen 4 days ago
Wageningen University, Wageningen, the …

Your input gene should be a character vector of entrez ids that you selected based on some criteria (e.g. significance); thus not a 2-column matrix.

Also note your choice for universe. The function enrichGO() pertforms a simple overrepresentation test of GO categories enriched in you input. As universe (background) you should therefore choose all genes that you measured (i.e. all genes measured in your RNA-seq or array experiment), thus another, longer character vector of entrez ids. If you don't set it yourselves, then all genes that have a GO annotation will be used as universe.

<<edit my answer because it was not fully correct).

ADD COMMENT

Login before adding your answer.

Traffic: 334 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6