Question: Bioconductor Graphite package : Cannot retrive pathways
gravatar for ES.67
3.2 years ago by
ES.6720 wrote:

Hello everyone

I am trying to use this package graphite for pathway analysis from gene expression data of Rice( Oryza sativa) . However, I cannot retrieve the pathways from kegg using this package. I am using this code osa <- pathways("Oryza sativa" , "kegg")

Firstly can it be used for organisms other than listed in pathwayDatabases() ? If so, how to do that ?

Thanks in advance.

pathways bioconductor R • 1.1k views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by ES.6720

What's the version of graphite you're using ? Non-human data has only been made accessible from version 1.14.

ADD REPLYlink written 3.2 years ago by Jean-Karim Heriche23k

I am using version 1.22.0.

ADD REPLYlink written 3.2 years ago by ES.6720
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