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Question: Using kegga and goana for Plants
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gravatar for jfreixas
11 days ago by
jfreixas0
jfreixas0 wrote:

I am trying to run a gene ontology analysis but my reference species is A.thaliana available here: org.At.tair.db. However, the function goana doesn't recognize species "At" and performs the GO enrichment against the human genome.

Kegga seems to recognize species "At" but I get the following error:

Error in kegga.default(de = DEGenes, universe = universe, ...) : 
  Pathways do not overlap with universe

Please any help is much appreciated.

 

 

ADD COMMENTlink modified 11 days ago by Gordon Smyth32k • written 11 days ago by jfreixas0
0
gravatar for Gordon Smyth
11 days ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

Actually, kegga() works fine with A. Thaliana. It does recognize species="At" and it does not require the org.At package. Have you read the documentation provided by help("kegga")?

The error you have received tells you that you have not passed the gene IDs correctly to kegga(). If you show us the output from

show(fit)

then we should be able to identify what your error is. Without seeing any code or output, it's impossible to diagnose.

 

On the other hand, goana() does not work for A. Thaliana, as I have explained here: [goana] function within edgeR not working for Arabidopsis

ADD COMMENTlink modified 11 days ago • written 11 days ago by Gordon Smyth32k
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