The editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

Question: [goana] function within edgeR not working for Arabidopsis
gravatar for jfreixas
12 months ago by
jfreixas0 wrote:

Hi All,

I am trying to run a gene ontology analysis using Arabidopsis annotation as reference (available at ""org.At.tair.db""). I am using the edgeR package particularly the function goana however when I specify the species (species=At) the function doesn't recognize the library org.At.tair.db. The coding is below, eny help would be much appreciated:


x<-read.delim("mygenes.csv", header=TRUE, sep=",")
mylist<-DGEList(counts=x[,3:8], genes=x[,2])

fit<-glmQLFit(y, design)
qlf <- glmQLFTest(fit, coef=2)
go <- goana(qlf, species="At")



Error in goana.default(de = DEGenes, universe = universe, ...) : package required but not not installed (or can't be loaded)


gene ontology • 303 views
ADD COMMENTlink modified 12 months ago by Gordon Smyth36k • written 12 months ago by jfreixas0
Answer: [goana] function within edgeR not working for Arabidopsis
gravatar for Gordon Smyth
12 months ago by
Gordon Smyth36k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth36k wrote:

goana() requires Entrez Gene IDs and, since there is no Entrez Gene ID-based annotation package for A. Thaliana, this means that you unfortunately can't use goana() with A. Thaliani.

The documentation provided by help("goana") tells you that uses goana() requires Entrez GeneIDs, and not Tair IDs. The help page says:

"goana uses annotation from the appropriate Bioconductor organism package. The species can be any character string XX for which an organism package is installed."

This tells you than goana() does not and cannot use org.At.tair.db. It instead looks for but, since there is no such package, this means that you can't use goana() for A. Thaliana. If you type help("alias2Symbol"), you will get a complete list of all the species that goana() works for.

ADD COMMENTlink modified 12 months ago • written 12 months ago by Gordon Smyth36k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 256 users visited in the last hour