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Question: how to run GO enrichment analysis for non-model organisms (errors when using hyperGTest)
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gravatar for zhaoran1124
5 months ago by
zhaoran11240 wrote:

I am trying to run the GO enrichment analysis for a subset of genes from my non-model organism. And my gene IDs are look like :"gene1036:10"

After creating a GOHyperGParams Object using the function GSEAGOHyperGParams, I run the hyperGTest function: 

params <- GSEAGOHyperGParams(name="test",
                             geneSetCollection=mygsc, 
                             geneIds = sub_genes, 
                             universeGeneIds = genes, 
                             ontology = "MF", 
                             pvalueCutoff = 0.05, 
                             conditional = FALSE,
                             testDirection = "over")

hyperGTest(params)

Then the error occurred:

Error in getUniverseHelper(probes, datPkg, entrezIds) : 
  After filtering, there are no valid IDs that can be used as the Gene universe.
  Check input values to confirm they are the same type as the central ID used by your annotation package.
  For chip packages, this will still mean the central GENE identifier used by the package (NOT the probe IDs).

 

I used my own GO annotation file, which is just a table with gene IDs and GO IDs. Do anyone know some tools for non-model organisms? Is it possible to run enrichment analysis based on a simple GO annotation table?

 

ADD COMMENTlink written 5 months ago by zhaoran11240

are your genes in mygsc in the same fashion as in genes? How do you  map from your ids of genes to gene ontology terms ?

ADD REPLYlink written 5 months ago by Lluís R370
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