Problems using customization in BINGO

[Marcio Luis Acencio]

Dear all,

I have been using BINGO for a long time and recently I have decided to use it to perform GO-based enrichment analysis of non-model transcriptomes.

In this case, i.e. non-model organism, I have prepared my own custom files -- reference and annotation files -- according to the guidelines presented at http://www.psb.ugent.be/cbd/papers/BiNGO/Customize.html. The ontology file (go-basic.obo) have been download from Gene Ontology.

In addition, I have updated some GO terms in my custom annotation files so that all terms are properly defined in go-basic.obo. To guarantee this "synchronization", I have performed multiple checks and have concluded that all GO terms in my annotation files are defined in the go-basic.obo.

Problem is that when I run BINGO, the following message appears:

WARNING: Some category labels in the annotation file are not defined in the ontology. Please check the compatibility of these files. For now, these labels will be ignored and calculations will proceed.

According to my checks, I can guarantee that these files are compatible.

I would like to know if this warning is a bug or if I am doing something wrong anyway.

Thank you in advance,

Marcio

[Tim Hull]

Hi,

Do you have some example files that demonstrate the problem? Having those would help in tracking this down.

Also, are you using BiNGO on Cytoscape 2.8.x or 3.x? In either case, could you test on the other version of Cytoscape to see if it happens and let us know what the result is?

If the issue happens on both Cytoscape 2.8.x and 3.x, this would be an issue with the BiNGO code. In that case, I would advise getting in touch with Steven Maere (steven...@psb.vib-ugent.be) who is the main developer on that project.

Hope this helps...

Tim

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[Namita Dube]

Hi Marcio,

     I am also facing warning message as you did. How did you solve this problem?

   

     Regards

     Namita