Question

Using kegga and goana for Plants

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jfreixas • 0

@jfreixas-15008

Last seen 6.2 years ago

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.

edger goana kegga • 2.4k views

ADD COMMENT • link updated 6.2 years ago by Gordon Smyth 50k • written 6.2 years ago by jfreixas • 0

score 0 · Answer 1 · 2018-02-13

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Gordon Smyth 50k

@gordon-smyth

Last seen 8 hours ago

WEHI, Melbourne, Australia

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 COMMENT • link 6.2 years ago Gordon Smyth 50k

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It's actually Ath not At and there are more subspecies of Arabidopsis. See here all the 3 letter codes for plant species: https://www.kegg.jp/kegg-bin/show_organism?category=Eudicots

ADD REPLY • link 4.5 years ago netbofia • 0

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My answer was correct as written. Please read the ?kegga documentation. kegga allows species names to be specified in either Bioconductor format (two letters) or KEGG format (three letters) via the two arguments species and species.KEGG. Also, the KEGG species names are all lowercase so your "Ath" is not correct.

ADD REPLY • link 4.5 years ago Gordon Smyth 50k