[BioC] RE : problem with makeGOGraph function

Samuel Rochette samuel.rochette.1 at ulaval.ca
Sun Mar 30 16:23:57 CEST 2014

Dear James,

thank you very much for your help. Although your suggestion makes a lot of sense, it seems that there is still a problem. When I type the command line that you suggested, the following error message appears: "Erreur dans newNodes[[i]] : indice hors limites". 

Please let me know if you have any other suggestion.


Samuel Rochette

De : James W. MacDonald [jmacdon at uw.edu]
Date d'envoi : 27 mars 2014 18:17
À : Samuel Rochette [guest]
Cc : bioconductor at r-project.org; Samuel Rochette
Objet : Re: [BioC] problem with makeGOGraph function

Hi Samuel,

On 3/27/2014 2:51 PM, Samuel Rochette [guest] wrote:
> Hi,
> I wish to produce a directed acyclic graph of a gene enrichment analysis that I performed using R GOstats package. For this, I wanted to use the makeGOGraph function, but it seems that there is a problem when using the yeast data base package "org.Sc.sgd.db".
> Here is the command line:
>> tree <- makeGOGraph(hits.list[[1]]$sys, Ontology="BP", removeRoot=TRUE,chip="org.Sc.sgd.db")
> where "hits.list[[1]]$sys" is a vector containing yeast genes.
>   -- output of sessionInfo():
> Here is the error message:
> "Erreur dans .get_eg_to_go_fun(mapfun, chip) :
>    either mapfun or chip must be specified
> De plus : Message d'avis :
> objet 'org.Sc.sgdGO2PROBE' introuvable
> DB-based version of  org.Sc.sgd.db  not found.
> Reverting to use of environment-based GO"
> It seems that there is something missing in the org.Sc.sgd.db package but I could not find out what exactly.

The problem here is that the function is really expecting that you are
using a chip-level package, rather than an organism level package. So
there is some functionality under the hood that tries to map chip probe
IDs to the respective GO IDs. Since you aren't doing that, you have to
supply a function that will do that for you.

Try this and see if it helps

myFun <- function(x){
tmp <- mget(x, org.Sc.sgdGO, ifnotfound = NA)
names(tmp) <- NULL
unlist(tmp, recursive = FALSE)

tree <- makeGOGraphs(hits.list[[1]]$sys, Ontology = "BP", removeRoot =
TRUE, mapfun = myFun)



> Thank you for your help!
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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