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using goProfiles (BioC) with non model organisms

Dear all,

During the last days I have been trying to figure out the best tool to perform gene enrichments and enrichment comparisons using GO.

It seems that the Bioconductor package goProfiles does exactly what I need. The problem is that I do not have a model organism; therefore I have no organism and annotation package available.

Looking in the manual of goProfiles, in the section "3.2.1 How can data be entered", I understand that for case like mine data can be entered as simple data frame, where are reported "GeneID", "Onology", "Evidence" (optional), "GOID".

> test.profiles
    GeneID Ontology Evidence       GOID
1 11589343       CC      IEA GO:0000156
2 11589345       CC      IEA GO:0003677
3 11588732       CC      IEA GO:0000179
4 11590726       CC      IEA GO:0003333
5 11591703       CC      IEA GO:0000156
6 11591901       CC      IEA GO:0003677
7 11591045       CC      IEA GO:0000156
8 11589721       CC      IEA GO:0000049

I tried to submit to the function basicProfile the data in such a format but I still get the same error telling me that the organism package has to be provided:

> basicProfile(test.profiles, onto = "CC", level=2)
Error in as.GOTerms.list(genelist, idType, orgPackage, anotPackage, na.rm = na.rm) : 
  'orgPackage' cannot be null. An organism annotation package (org.Xx.eg.db) must be provided

I guess I am missing something here. Is there anyone who could help me to understand my mistake?

annotation r bioconductor
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updated by Ram Ram • written by dago dago

As it says, it needs an annotation for your organism so it can determine the background probabilities. What are the GeneIDs from? If these are IDs from a related organism then you might be able to use the annotation for it.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

I create my own organism package with AnnotationForge. But what it is needed for goProfiles is the dataset org.Xx.egGO, which is not created w AnnotationForge. Any idea where I could look up a way to create this dataset and include it in my organism package?

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updated by Ram Ram • written by dago dago

Presumably you could use the same annotation. I'm assuming that the portion you're using now is just comprised of differentially expressed features.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

Thanks for your answer.

I can see that:

> colnames(org.Hs.egGO)
[1] "gene_id"  "go_id"    "Evidence" "Ontology"

Therefore, I assume that this dataset is a dataframe containing the above information. My problem is that I do not know which procedure to follow to include this datraframe as org.Xx.egGO in the package of my oprganism, which I created with makeOrgPackage() from AnnotationForge

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updated by Ram Ram • written by dago dago

It's not a data.frame, it just has a colnames accessor. That's a Go3AnnDbBimap object. I've never had to make one myself. Realistically speaking, it might be easier to just use a different package that lets you manually supply a background set of IDs.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

I have the same problem. Did you find a solution?

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updated by Ram Ram • written by cpcantalapiedra cpcantalapiedra

1 answer

I made it work with the idType parameter in basicProfile(), like:

basicProfile(GOTermsFrame, idType = "GOTermsFrame", onto = "BP", level = 2)
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updated by Ram Ram • written by cpcantalapiedra cpcantalapiedra

Hey cpcantalapiedra!

I tried using your advice, as I also use three non-model organisms with already several annotated GO terms per Gene ID - and my aim is to compare all three organisms with each other.

If I create the basic profile the way you supposed, I got 0 frequencies - did you have that as well? In which format did you upload your data initially before building the functional profile? I feel like my tables just might not have the right format, which is:

GeneID Ontology Evidence       GOID 
1 110826457       MF      IEA GO:0004888

But even if I calculated the frequencies (occurrence of GO term in data frame Cafin) manually, creating the mergedProfileList results in the error:

Error in !emptyCats : invalid argument type

Can anybody help me?

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updated by Ram Ram • written by Maria Scheel • Maria Scheel

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