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

library(edgeR)
source("https://bioconductor.org/biocLite.R")
biocLite("org.At.tair.db")
library("org.At.tair.db")

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

group<-factor(c(1,1,1,2,2,2))
design<-model.matrix(~group)
fit<-glmQLFit(y, design)
qlf <- glmQLFTest(fit, coef=2)
go <- goana(qlf, species="At")

 

ERROR:

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

 

ADD COMMENTlink modified 6 months ago by Gordon Smyth34k • written 6 months ago by jfreixas0
0
gravatar for Gordon Smyth
6 months ago by
Gordon Smyth34k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth34k 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 org.XX.eg.db is installed."

This tells you than goana() does not and cannot use org.At.tair.db. It instead looks for org.At.eg.db 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 6 months ago • written 6 months ago by Gordon Smyth34k
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