Hi,

I was trying to use topGO to find over-representation of some selected genes. I don't have probe ids, just the gene symbols for both the selected genes and the gene universe. For the topGO object, I have:

sampleGOdata <- new("topGOdata",
                      description = "Simple session", ontology = "BP",
                      allGenes = mygeneUniverse, geneSel = myselectedGenes,
                      nodeSize = 10,
                      annot = annFUN.db)

How can I create the annot object so that I can create my topGO object?

thanks!!

Hi Brian,

this is a bit complicated, you need to define something like:

annot=annFUN.org, mapping="org.Mm.eg.db", ID = "ensembl"

in the call of "new" (for ENSEMBL IDs in this case). You can find a worked example in some teaching material of mine:

http://www-huber.embl.de/users/klaus/Teaching/DESeq2Predoc2014.html#gene-ontology-enrichment-analysis

Here are  the link to the source of this html:

http://www-huber.embl.de/users/klaus/teaching.html#differential-expression-analysis-of-rna-seq-predoc-course-2014

Cheers.

Bernd