[BioC] topGO question

[Adrian Alexa]

Hi Heike,

it seems that there is a problem with the go_list object. It should be
a list of character vectors. However, it is hard to tell what is wrong
with just the information you provided. Please also post the session
info such that we know which version of the software are you using.

The error is with the annFUN.gene2GO() function. if the go_list is
correct, than the following line should pass without error:

go2genes <- annFUN.gene2GO(whichOnto = "MF", gene2GO = go_list)

If you get an error here, can you post the results of the following lines:

allGO = unlist(go_list, use.names = FALSE)
str(allGO)
sum(is.na(allGO))
sum(is.null(allGO))


Regards,
Adrian






On Fri, Sep 12, 2008 at 11:42 AM, Heike Pospisil
<pospisil at zbh.uni-hamburg.de> wrote:
> Hello list,
>
> I am trying to use topGO for GO enrichment analysis. I have data from an
> array which is still not supported by BioC (maize array).
>
> I have a mapping of genes to GO terms named go_list:
>
> $TM00000001
> [1] "GO:0009058" "GO:0016757"
>
> $TM00000002
> [1] "GO:0003700" "GO:0007275" "GO:0005634" "GO:0009414" "GO:0016563"
> [6] "GO:0009737" "GO:0045449" "GO:0010072" "GO:0046982" "GO:0009651"
> [11] "GO:0009733" "GO:0009723" "GO:0009734" "GO:0048527" "GO:0042803"
> [16] "GO:0009867" "GO:0010150" "GO:0009825" "GO:0009908" "GO:0003713"
> [21] "GO:0051607" "GO:0009790" "GO:0010014" "GO:0048467" "GO:0030528"
> [26] "GO:0009741" "GO:0009735" "GO:0010089" "GO:0009834" "GO:0009901"
> [31] "GO:0009611" "GO:0008361" "GO:0009416" "GO:0009620" "GO:0009744"
> [36] "GO:0009753" "GO:0009751" "GO:0010199"
>
> Moreover, the geneList is the named factor that indicates which genes are
> interested:
>> str(geneList)
> Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
> - attr(*, "names")= chr [1:56321] "MZ00000001" "MZ00000002" "MZ00000003"
> "MZ00000004" ...
>
> I have used annFUN.gene2GO  as an annotation function:
>
> GOdata<-new("topGOdata",ontology="MF",allGenes=geneList,annot=annFUN.gene2GO,gene2GO=go_list)
>
> Unfortunately,  I got the following error message:
> Building most specific GOs .....Error in order(allGO) : argument 1 is not a
> vector
>
> Does anybody have an idea what is wrong in my code?
>
> Thanks and best,
> Heike
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>