Hello all,

I've been using the topGO package from the bioconductor to do GSEA. Today I compared the results of topGO with those using panther with defaults. I general they are more or less the same but some of the GOTerms from panther GSEA are more meaningful for my analysis. I could use panther but I would prefer to use R/Bioconductor so I can pipeline my analysis more easily.

This is the code I used in R:

selection <- function(allScore){return(allScore < 0.05)}

GOdata <- new("topGOdata",
               ontology      = "BP",
               allGenes      = IdentifiedGenesVector, 
               geneSel       = selection,
               nodeSize      = 5,
               annotationFun = annFUN.org,
               mapping       = "org.Hs.eg.db",
               ID            = "symbol")

And this are the first few genes I want to analyze:

head(IdentifiedGenesVector)
RP11-27K13.3   AC021224.1        ALCAM      ALDH1A1        DHRS9        IFI27
         0.04         0.04         0.04         0.04         0.04         0.04

Can I use panther's mapping in topGO?

Is there any other gene-to-GO mapping that I could try?

Is there a generally accepted mapping to use?

I have seen in many posts that many people cast their own mapping list but I'm not sure how I would do this.

Thanks a lot, Jose.